Spectroscopic methods to detect and characterize microorganisms

ABSTRACT

Methods and systems for Resonant Raman spectroscopy are provided. Methods according to certain embodiments include irradiating a sample with a monochromatic light source at a first irradiation intensity and a second irradiation intensity, determining the intensity of one or more of the Resonant Raman scattering and fluorescence scattering at the first irradiation intensity and second irradiation intensity, calculating a rate of change of one or more of the intensity of Resonant Raman scattering and fluorescence in response to the change in irradiation intensity from the first irradiation intensity to the second irradiation intensity and comparing one or more of the rate of change in the intensity of Resonant Raman scattering and the rate of change in the intensity of fluorescence scattering with the rate of change in the irradiation intensity by the monochromatic light source to determine the Resonant Raman response of the sample. Methods also include determining the presence or absence of a microorganism in a sample and correcting for variations associated with measurement instrumentation (e.g., monochromatic light source) and variations associated with the sample (e.g., fluorescence from non-target compounds). Also provided are methods for determining the antimicrobial susceptibility of a microorganism to an antimicrobial agent as well as methods for characterizing a phenotype of an unknown microorganism in a sample. Systems for practicing the subject methods are also provided.

CROSS-REFERENCE

This application claims the benefit of U.S. Provisional PatentApplication No. 62/614,216, filed Jan. 5, 2018, and U.S. ProvisionalPatent Application No. 62/473,876, filed Mar. 20, 2017, whichapplications are incorporated herein by reference in their entireties.

INTRODUCTION

Raman spectroscopy is used to characterize the vibrational, rotationaland other low frequency molecular motions of compounds and is commonlyemployed to provide data for identifying the presence of particularmolecules in a sample. Raman scattering is the inelastic scattering ofmonochromatic light (e.g., ultraviolet, visible or near infrared) wherethe light interacts with molecular vibrations resulting in a shift inenergy by the scattered photons. The application of this method to thestudy of the conformations of biological molecules has developed onlyslowly because of numerous difficulties such as the great complexity ofthe spectra, poor quality spectra obtained from dilute solution and thelarge volumes needed.

The strong enhancement (10 to 10⁶ fold) observed when the radiation usedto excite the Raman spectra lies in an electronic absorption band of achromophore allows the analysis of specific vibrational modes of thechromophore, even if it is included in a complex biological medium atvery low concentration. Since many natural chromophores play importantroles in many biological activities, Raman spectroscopy is often used toprobe different biological processes. Detection and structural analysisof very small concentrations of biological pigments is possible in thepresence of large amounts of non-absorbing species.

SUMMARY

Aspects of the present disclosure include methods and systems forResonant Raman spectroscopy. Methods according to certain embodimentsinclude irradiating a sample with a monochromatic light source at afirst irradiation intensity and a second irradiation intensity,determining the intensity of one or more of the Resonant Ramanscattering and fluorescence scattering at the first irradiationintensity and second irradiation intensity, calculating a rate of changeof one or more of the intensity of Resonant Raman scattering andfluorescence scattering in response to the change in irradiationintensity from the first irradiation intensity to the second irradiationintensity and comparing one or more of the rate of change in theintensity of Resonant Raman scattering and the rate of change in theintensity of fluorescence scattering with the rate of change in theirradiation intensity by the monochromatic light source to determine thespectroscopic response of the sample. In some embodiments, thespectroscopic response (e.g., Resonant Raman scattering and/orfluorescence scattering) of the sample is indicative of a physicalchange over time in the sample. In other embodiments, the spectroscopicresponse of the sample is indicative of a chemical change over time inthe sample. In still other embodiments, the spectroscopic response ofthe sample is indicative of the presence of an actively metabolizingmicroorganism in the sample. In some embodiments, the monochromaticlight source is a laser. In some embodiments, the sample includes ahydrophobic compound and an albumin protein. For example, thehydrophobic compound may be incorporated into the albumin protein. Thehydrophobic compound is, in certain instances, a carotenoid, such aslycopene. In certain embodiments, the sample includes a hydrophobiccompound, an albumin protein and a reducing agent. The reducing agentis, in certain instances, glutathione or a derivative thereof. In otherembodiments, the sample includes a hydrophobic compound, an albuminprotein and a free radical scavenger. The free radical scavenger is, incertain instances, bilirubin or a derivative thereof.

In some instances, methods include irradiating the sample over aplurality of irradiation intensities by the monochromatic light sourceover a period of time and determining one or more of a rate of change inthe intensity of Resonant Raman scattering and a rate of change in theintensity of fluorescence scattering. In other instances, methodsinclude irradiating a first sample over a plurality of intensities bythe monochromatic light source for a period of time and determining oneor more of a rate of change in the intensity of Resonant Ramanscattering and a rate of change in the intensity of fluorescencescattering for the first sample; calculating a net signal for the firstsample by comparing one or more of a normalized rate of change in theintensity of Resonant Raman scattering and a normalized rate of changein the intensity of fluorescence scattering for the first sample with anormalized rate of change in the irradiation intensity of the firstsample by the monochromatic light source; irradiating a second sampleover a plurality of intensities by the monochromatic light source forthe period of time and determining one or more of a rate of change inthe intensity of Resonant Raman scattering and a rate of change in theintensity of fluorescence scattering for the second sample; andcalculating a net signal for the second sample by comparing one or moreof a normalized rate of change in the intensity of Resonant Ramanscattering and a normalized rate of change in the intensity for thesecond sample with a normalized rate of change in the irradiationintensity of the second sample by the monochromatic light source. Insome embodiments, methods further include comparing the net signal forof the first sample with the net signal for the second sample. Based onthe compared calculated net signal, methods may include one or moreof: 1) determining that the first sample and second sample aredifferent; 2) determining that the first sample comprises a differentgaseous composition from the second sample; and 3) determining that thefirst sample or the second sample comprises actively metabolizingmicroorganisms.

Aspects of the present disclosure also include methods for determiningthe presence of a microorganism in a sample. Methods according tocertain embodiments, include combining in a sample holder the samplewith a reagent that contains albumin with an incorporated ligand;irradiating the sample with a monochromatic light source that isabsorbed by the ligand, with either an invariant light intensity or onethat varies over time focused at an interface between the sample and asurface of the sample holder; collecting scattered light from theirradiated sample and measuring a Raman signal and a fluorescence signalfrom the scattered light at a plurality of different times; calculatinga rate of change in intensity of the Raman signal and fluorescencesignal for the sample over time; correcting the calculated rates ofchange in the intensities of the Raman signal and the fluorescencesignal to obtain a net signal; and determining the presence of amicroorganism in the sample based on a comparison of the net signalversus one or more preset thresholds.

In some embodiments, the one or more present thresholds are set byimplementing the method on one or more control samples that contains aninoculum in an amount at a lower limit of concentration in a clinicallyinfected sample.

In some instances, correcting the rate of change in the intensities ofthe Raman signal and the fluorescence signal includes characterizing aspectral output from a standard sample. In other instances, correctingthe rate of change in the intensities of the fluorescence signalincludes characterizing a fluorescence output from the reagent.

In certain embodiments, correcting the rate of change in the intensitiesof the Raman signal and the fluorescence signal includes determining arate of change in total output from a standard reference sample andcalculating a net signal as the rate of change in the intensity of theResonant Raman scattering minus the rate of change in the intensity ofResonant Raman scattering from the standard sample.

In other embodiments, correcting the rate of change in the intensitiesof the Raman signal and the fluorescence signal includes determining arate of change in the intensity of fluorescent scattering from astandard reference sample and calculating a net signal as the rate ofchange in the intensity of the Resonant Raman scattering minus the rateof change in the intensity of fluorescent scattering from the standardsample.

In some embodiments, methods further include pretreating the albuminprior to incorporating the ligand, such as for example by contacting thealbumin with a reducing agent (e.g., glutathione). The reducing agentis, in certain instances, sufficient to reduce the disulfide bonds inthe albumin. In other embodiments, the albumin is pretreated with adisulfide crosslinking agent. In some instances, the disulfidecrosslinking agent includes a core that is cleaved by enzymes or ametabolite produced by the microorganism in the sample. In certaininstances, the disulfide crosslinking agent is a compound of Formula(I):

Aspects of the present disclosure also include determining the presenceof a microorganism (e.g., an actively metabolizing microorganism) in asample with Resonant Raman scattering. Methods according to certainembodiments include irradiating a sample over a plurality of intensitiesby a monochromatic light source for a period of time and calculating arate of change in the intensity of Resonant Raman scattering for thefirst sample; calculating a net signal for the sample by comparing anormalized rate of change in the intensity of Resonant Raman scatteringfor the sample with a normalized rate of change in the irradiationintensity of the sample by the monochromatic light source; anddetermining the presence of a microorganism in the sample based on thenet signal for the sample. In certain instances, a microorganism isdetermined to be present when the net signal of the sample is above apredetermined threshold. In other embodiments, determining the presenceof a microorganism includes: irradiating a first sample over a pluralityof intensities by a monochromatic light source for a period of time andcalculating a rate of change in the intensity of Resonant Ramanscattering for the first sample; calculating a net signal of the firstsample by comparing a normalized rate of change in the intensity ofResonant Raman scattering for the first sample with a normalized rate ofchange in the irradiation intensity of the first sample by themonochromatic light source; irradiating a second sample over a pluralityof intensities by the monochromatic light source for the period of timeand determining a rate of change in the intensity of Resonant Ramanscattering for the second sample; calculating a net signal of the secondsample by comparing a normalized rate of change in the intensity ofResonant Raman scattering for the second sample with a normalized rateof change in the irradiation intensity of the second sample by themonochromatic light source; and determining the presence of amicroorganism in one or more of the first sample or the second sample bycomparing the net signal of the first sample with net signal of thesecond sample. In some instances, a microorganism is determined to bepresent in the second sample when the net signal of the second sample isgreater than the net signal of the first sample. In other instances, amicroorganism is determined to be present in the first sample when thenet signal of the first sample is greater than the net signal of thesecond sample.

Aspects of the present disclosure also include determining the presenceof a microorganism (e.g., an actively metabolizing microorganism) in asample by fluorescence spectroscopy. Methods according to certainembodiments include irradiating a sample by a monochromatic light sourcefor a period of time and detecting fluorescence from the sample over theperiod of time; calculating a rate of change of the fluorescence due tothe presence of a microorganism by comparing a normalized rate of changein the intensity of the detected fluorescence produced by the samplewith a normalized rate of change of fluorescence produced by a control;and determining the presence of a microorganism in the sample based onthe calculated changes in the fluorescence of the sample compared topreset thresholds.

In determining the presence of a microorganism (e.g., an activelymetabolizing microorganism) in a sample, methods include irradiating thesample in a sample holder. In some embodiments, the sample holder is acontainer, for example a cuvette, vial, planar substrate, ormicrofluidic device. The sample container is, in certain instances, aglass vial. In some embodiments, the glass vial has walls with azwitterionic coating, such as a zwitterionic silane coating. In theseembodiments, the sample may be irradiated at an interface between thesample and a surface of the sample holder (e.g., the container wall),such as by focusing the monochromatic light source at a position at theinterface between the sample and the surface of the sample holder (e.g.,container wall). In some instances, the monochromatic light is focusedat a position of from 0.01 mm to 2 mm from the surface of the surface ofthe sample holder (e.g., container wall), such as at about 0.2 mm fromthe surface of the surface of the sample holder (e.g., container wall).The monochromatic light may be focused for example, with a collimatingoptics (e.g., including a collimating lens).

Aspects of the present disclosure also include a method for calculatingsignal-to-noise ratio. In some embodiments, methods include irradiatinga first sample over a plurality of intensities by a monochromatic lightsource for a period of time and determining a rate of change in theintensity of Resonant Raman scattering for the first sample; calculatingan average rate of change in the intensity of Resonant Raman scatteringby the first sample to give a first average rate of change; calculatinga standard deviation for the first average rate of change; irradiating asecond sample over a range of intensities by the monochromatic lightsource for the period of time and determining a rate of change in theintensity of Resonant Raman scattering for the second sample;calculating an average rate of change in the intensity of Resonant Ramanscattering by the second sample to give a second average rate of change;calculating a standard deviation for the second average rate of change;subtracting the second average rate of change from the first averagerate of change to give a signal average rate of change; adding the firststandard deviation and the second standard deviation to give a signalstandard deviation; and dividing the signal average rate of change bythe signal standard deviation to determine a signal-to-noise ratio forResonant Raman response.

Aspects of the present disclosure further include a method fordetermining and correcting for variations in optical measurementinstrumentation (e.g., thermal drift of a monochromatic light source,changes in positioning of optical components, etc.) as well asvariations in the sample (e.g., fluorescence from non-target compounds).In some embodiments, methods include irradiating a reference compositionover a plurality of intensities by the monochromatic light source forthe period of time and determining one or more of a rate of change inthe intensity of Resonant Raman scattering and a rate of change in theintensity of fluorescence scattering, wherein the reference compositioncomprises a reference compound that exhibits no change in the intensityof Resonant Raman scattering or fluorescence scattering in response tothe change in irradiation intensity by the monochromatic light source;and calculating a net signal of the reference composition by comparingone or more of the rate of change in the intensity of Resonant Ramanscattering and the rate of change in the intensity of fluorescencescattering for the reference composition with the rate of change in theirradiation intensity of the reference composition by the monochromaticlight source. In certain instances, methods further include irradiatinga sample over a range of intensities by a monochromatic light source fora period of time and determining one or more of a rate of change in theintensity of Resonant Raman scattering; and obtaining a net signal bycorrecting the determined rate of change in the intensity of ResonantRaman scattering of the sample with the rate of change of irradiationintensity of the sample by the monochromatic light source to produce acorrection factor; and subtracting the correction factor from thedetermined rate of change in the intensity of Resonant Raman scatteringfor the sample.

Aspects of the present disclosure further include a method fordetermining the antimicrobial susceptibility of a microorganism to anantimicrobial agent with Resonant Raman scattering. In some embodiments,methods include irradiating a plurality of samples, each samplecomprising a microorganism and an antimicrobial agent over a pluralityof intensities by the monochromatic light source for a period of timeand determining a rate of change in the intensity of Resonant Ramanscattering for each irradiated sample, wherein each sample comprises thesame concentration of microorganism and different concentrations ofantimicrobial agent; calculating a net signal for each sample bycomparing a normalized rate of change in the intensity of Resonant Ramanscattering for each sample with a normalized rate of change in theirradiation intensity of each sample by the monochromatic light source;and determining the susceptibility of the microorganism to theantimicrobial agent based on the net signal of the plurality of samples.In some instances, methods further include plotting the net signal foreach sample as a function of the log of the concentration ofantimicrobial agent in each sample. In certain instances, methods mayalso include determining the minimum inhibitory concentration ofantimicrobial agent by determining the concentration that first exhibitsa decrease in the plotted net signal. In other instances, methods mayalso include determining the maximal bactericidal concentration of theantimicrobial agent by determining the concentration that first exhibitsan increase in the plotted net signal. In other embodiments, methodsfurther include determining the metabolic activity of the microorganismin each sample based on the net signal for each sample. In someinstances, methods include determining the concentration ofantimicrobial agent that exhibits a decrease in metabolic activity. Inother instances, methods include determining the concentration ofantimicrobial agent that exhibits an increase in metabolic activity.

Aspects of the present disclosure further include a method fordetermining the antimicrobial susceptibility of a microorganism to anantimicrobial agent by fluorescence spectroscopy. In some embodiments,methods include irradiating a plurality of samples each having amicroorganism and an antimicrobial agent with a monochromatic lightsource for a period of time and detecting fluorescence from each of theirradiated samples over the period of time, where each sample has thesame concentration of microorganism and different concentrations ofantimicrobial agent; calculating a rate of change of the fluorescence ineach sample by comparing a normalized rate of change in the intensity ofthe detected fluorescence produced by each sample with a normalized rateof change of fluorescence produced by a control; and determining thesusceptibility of the microorganism to the antimicrobial agent based onthe calculated rate of change of the fluorescence of the plurality ofsamples. In some embodiments, methods include irradiating each of thesamples over a plurality of intensities of the monochromatic lightsource.

Each sample in these embodiments may include the same concentration ofmicroorganism, for example, a concentration of microorganism of 10colony forming units (CFUs) or more, such as 14 CFUs or more. In certainembodiments, the samples of microorganisms are prepared by preparing acomposition having a predetermined concentration of microorganism (e.g.,100 CFUs) and aliquoting a predetermined volume of the microorganismcomposition into each sample such that each sample has the sameconcentration of microorganism. In embodiments, the concentration ofantimicrobial agent in the plurality of samples ranges from aconcentration that is below the minimum inhibitory concentration of theantimicrobial agent to a concentration that is greater than the minimumbactericidal concentration of the antimicrobial agent. The antimicrobialagent may be incubated with the microorganisms in the sample for apredetermined period of time before irradiating with the monochromaticlight source, such as for 10 minutes or more, or 20 minutes or more.

Aspects of the present disclosure further include a method forcharacterizing a phenotype of an unknown microorganism with ResonantRaman scattering. In some embodiments, methods include irradiating witha monochromatic light source a sample comprising a microorganism, acrosslinking agent and an albumin protein over a plurality ofintensities by the monochromatic light source for a period of time anddetermining a rate of change in the intensity of Resonant Ramanscattering; calculating a net signal for the sample by comparing anormalized rate of change in the intensity of Resonant Raman scatteringfor the sample with a normalized rate of change in the irradiationintensity of the sample by the monochromatic light source; anddetermining crosslink cleavage of the albumin protein based on the netsignal of the sample, wherein the extent of crosslink cleavage isindicative of the phenotype of the microorganism.

Aspects of the present disclosure further include a method forcharacterizing a phenotype of an unknown microorganism by fluorescencespectroscopy. In some embodiments, methods include irradiating with amonochromatic light source a sample comprising a microorganism, acrosslinking agent and an albumin protein for a period of time anddetecting fluorescence from the sample over the period of time;calculating a rate of change of the fluorescence by comparing anormalized rate of change in the intensity of the detected fluorescenceproduced by the sample with a normalized rate of change of fluorescenceproduced by a control; and determining crosslink cleavage based on thecalculated rate of change of fluorescence of the sample, wherein theextent of crosslink cleavage is indicative of the phenotype of themicroorganism. In some embodiments, methods include irradiating thesample over a plurality of intensities of the monochromatic lightsource.

In embodiments, the crosslinking agent may be a disulfide crosslinker.In some instances, the crosslinking agent is a glutamic acid derivative.In certain embodiments, the crosslinking agent is a compound of Formula(I):

The crosslinking agent may be present in the sample in an amount wherethe molar ratio of crosslinking agent to albumin protein is from 1:10 to10:1, for example a molar ratio of crosslinking agent to albumin proteinof about 1:2. In embodiments, an increase over time in the net signal ofthe sample is indicative that the microorganism produces a metabolitethat cleaves one or more crosslinks in the albumin protein. Based onthis, the phenotype of the microorganism may be characterized.

Systems for practicing the subject methods having a monochromatic lightsource and a detector for detecting Resonant Raman scattering orfluorescence are also provided. In some embodiments, the monochromaticlight source is a laser. For example, the laser may be a Nd:YAG laser,such as a frequency doubled Nd:YAG laser that outputs light at 532 nm.In some instances, the detector is a charged coupled device (CCD). Insome embodiments, systems further include a sample container. The samplecontainer, for example, may be a glass vial. In some embodiments, theglass vial has walls with a zwitterionic coating, such as a zwitterionicsilane coating. In these embodiments, the subject systems are configuredto irradiate the sample at an interface between the sample and thecontainer wall, such as by focusing the monochromatic light source at aposition at the interface between the sample and the container wall. Insome instances, the monochromatic light is focused at a position of from0.01 mm to 2 mm from the surface of the container wall, such as at about0.2 mm from the surface of the container wall. These systems may alsoinclude an optical adjustment component to focus the monochromatic lightsource at the interface between the sample and the container wall, suchas a collimating lens.

BRIEF DESCRIPTION OF THE FIGURES

The invention may be best understood from the following detaileddescription when read in conjunction with the accompanying drawings.Included in the drawings are the following figures:

FIG. 1 depicts normalized rate of change of Resonant Raman intensityfrom lycopene plotted against the normalized rate of change of laserintensity according to certain embodiments.

FIG. 2 depicts variation in the nonlinearity coefficient with the amountof dissolved gases (and super saturated gases) present in the liquidaccording to certain embodiments.

FIG. 3 depicts average Resonant Raman scattering peak height from 4uninfected control samples and 3 samples infected with 10 CFUs of S.aureus.

FIG. 4 depicts average Resonant Raman scattering peak height from 4uninfected control samples and 3 samples infected with 10 CFUs of S.aureus, each composition including 1 μM of bilirubin.

FIG. 5 depicts the signal-to-noise ratio of control samples and thosewith 10 CFU of S. aureus according to certain embodiments.

FIG. 6 depicts a plot of the signal for Resonant Raman scatteringestimated at t=600 seconds, plotted as a function of added bilirubinaccording to certain embodiments.

FIG. 7 depicts the variation of the signal to noise ratio forcompositions having different amounts of bilirubin plotted as a functionof time of experiment according to certain embodiments.

FIG. 8 depicts the variation in the timescale at which thesignal-to-noise ratio is optimized with the amount of bilirubin presentin the assay according to certain embodiments.

FIGS. 9A-9B depict the variation in the measured values for 4 uninfectedand 3 infected samples, as a function of bilirubin content. FIG. 9Adepicts the raw data values as measured. FIG. 9B depicts data valuescorrected for the observed drift in laser power.

FIG. 10 depicts determining instrument stability using normalized rateof change of Resonant Raman scattering of a reference composition ascompared to the normalized rate of change of the photodetector shuttertime according to certain embodiments.

FIG. 11 depicts a layer of a sample chamber according to certainembodiments.

FIG. 12 depicts a flowchart for minimizing thermal effects on laserpower according to certain embodiments.

FIG. 13 depicts a flowchart for checking a system for thermalinstability according to certain embodiments.

FIG. 14 depicts a YCAL test for checking a system for thermalinstability according to certain embodiments.

FIG. 15 depicts a flowchart for control steps to minimize thermalfluctuations during system operation according to certain embodiments.

FIG. 16 depicts the relationship of signal magnitude from samples havingdifferent concentrations of reducing agent according to certainembodiments.

FIG. 17 depicts the relationship of signal magnitude and incubation timeat a predetermined measurement time according to certain embodiments.

FIG. 18 depicts the relationship between the rate of change of the Ramanpeak height and the laser exposure time according to certainembodiments.

FIG. 19 depicts the relationship between the confidence interval of theNIST profile and distance from sample-container interface and focal spotof light irradiation according to certain embodiments.

FIG. 20 depicts the relationship between Raman intensity profile andcollimating lens position from the sample container according to certainembodiments.

FIG. 21 depicts the relationship between the slope of uninfected controlsamples and the focal spot position of the monochromatic light sourcefrom the edge of the sample-container interface according to certainembodiments.

FIG. 22A depicts the signal-to-noise ratio of Raman spectra obtained forsamples in Zwitterion coated glass vials according to certainembodiments. FIG. 22B depicts the signal-to-noise ratio of Raman spectraobtained for samples in uncoated glass vials according to certainembodiments.

FIG. 23 depicts the relationship between signal-to-noise ratio and focalspot distance from sample-container interface according to certainembodiments.

FIG. 24 depicts the Lieber method for fitting a 5^(th) order polynomialto a spectra having contributions from Raman peaks and backgroundfluorescence according to certain embodiments.

FIG. 25A depicts the relationship of signal-to-noise ratio with theslope and according to certain embodiments. FIG. 25B depicts therelationship of signal-to-noise ratio with the confidence interval ofslope according to certain embodiments.

FIG. 26A depicts amplitude of Raman peaks, aggregated for the 4uninfected control samples and the 3 infected samples according tocertain embodiments. FIG. 26B depicts the estimated rate of change foruninfected samples and infected samples from the area under the curve.FIG. 26C depicts the estimated signal-to-noise ratio of uninfected andinfected samples.

FIG. 27 depicts the estimated slopes, aggregated for control andinfected samples and corrected for variation observed in an NISTstandard according to certain embodiments.

FIG. 28A depicts the estimated rate of change for the uninfected andinfected samples, estimated from the area under the curve according tocertain embodiments. FIG. 28B signal-to-noise ratio, estimated as thesignal divided by the rms standard deviation of the rate of change ofuninfected and infected samples according to certain embodiments. FIG.28C depicts signal, as a function of time for this sample set in whichthe bacteria has been centrifuged and removed according to certainembodiments.

FIG. 29A depicts the rate of change of Raman peaks in clinical samplesaccording to certain embodiments. FIG. 29B depicts amplitude of theRaman peaks for a set of tests completed on clinical samples with addedplasma from different patients according to certain embodiments.

FIG. 30 depicts the relationship between the rate of change of Ramanpeaks and time to positivity in a blood culture test according tocertain embodiments.

FIG. 31A depicts the change in signal magnitude of samples havingdifferent bacterial concentration in clinical samples according tocertain embodiments. FIG. 31B depicts the signal strength at 1000seconds for clinical samples having different bacterial concentrationaccording to certain embodiments.

FIG. 32A depicts the measured slope of Raman intensity as a functionalof antimicrobial (vancomycin) concentration according to certainembodiments. FIG. 32B depicts the time taken for the tested samples tobecome cloudy.

FIG. 33A depicts the effect of absorbance at 650 nm for a peptidecrosslinker compound that contains two disulfide bonds according tocertain embodiments. FIG. 33B depicts the increase in Raman signal overtime as a function of concentration of microorganism.

FIG. 34 depicts the increase in Raman signal as a function of molarratio of added disulfide crosslinker according to certain embodiments.

FIG. 35A depicts fluorescence measurements aggregated for the 3uninfected control samples according to certain embodiments. FIG. 35Bdepicts the signal-to-noise ratio for fluorescence detection, estimatedas the signal divided by the rms standard deviation of the rate ofchange of uninfected and infected samples according to certainembodiments.

SELECT DEFINITIONS

As used herein, “Raman scattering” and other similar terms and/orphrases, refer to any method whereby light incident on a sample at afixed wavelength is scattered at other wavelengths. The scattering maybe by an incoherent process due to the absorption of the incident photonby the excitation of the structure from an initially lower (the groundstate) to a higher vibrational level, and subsequent relaxation down toa different ground state level.

As used herein, the “Raman band” and similar terms and/or phrases referto the spectral profile (e.g. intensity versus frequency) correspondingto the Raman scattering from a particular chemical bond within amolecule. It is understood that each chemical bond manifests as a Ramanband at distinct frequencies and that in some cases, these Raman bandsmay overlap, making them difficult to distinguish. Further, it isunderstood that the Raman cross section of a chemical bond is a constantthat defines the intensity of the corresponding Raman peak. Furthermore,it is understood that this cross section can change with wavelengthand/or with resonance. Such a resonance change occurs during resonantRaman enhancement.

As used herein, it is understood that the “Raman spectrum” of a sample,and similar terms and/or phrases, refer to the sum of all the Ramanbands, and the relative heights on individual Raman bands in a Ramanspectrum is proportional to the relative abundance of the correspondingchemical bonds multiplied by their Raman cross section.

As used herein, “absorption” and similar terms and or phrases refer toany method wherein incident light is absorbed by a sample of interest.The incident photon may interact with a structure by any number ofmechanisms, including the excitation of outer electrons (e.g.corresponding to the absorption of UV or visible radiation), or theexcitation of the molecule into higher vibrational/rotational energystates.

As used herein, “Resonant Raman scattering” and similar phrases and/orterms, refers to a process that is understood to be a special type ofRaman scattering that involves the excitation of a molecule from aninitial ground state to a real excited state that corresponds to a realvibrational state. Thus, for the purpose of the present discussion,resonant “Raman enhancement” (or “resonance Raman”), and other similarterms and/or phrases, refer to any method whereby the Raman crosssection of a particular band is enhanced by the strong opticalabsorption.

As used herein, “Resonant Raman Nonlinearity (RRNL)” refers to the slopeof the trace between the rate at which the intensity of the ResonantRaman peak changes (plotted on the Y axis) and the rate at which theintensity of the incident laser beam changes (plotted on the X axis).

As used herein, “net signal” refers to the rate of change of theintensity of one or more of the Raman scattering or fluorescencescattering after correction for variations associated with theinstrument (e.g., drift in the monochromatic light source, drift inoptical components such as collimating optics) and/or in the sample vial(e.g., fluorescence from non-target compounds). In some embodiments,“net signal” is related to Resonant Raman Nonlinearity (RRNL) as definedabove in that when the RRNL=1, Net Signal=0 and when Net Signal is lessthan 0, then RRNL is <1.

As used herein, “vial” and other similar terms and/or phrases refer to atest container that contains, e.g., the test sample, along with anyother components of the assay. It is understood that the vial can beconstructed out of any suitably transparent material, such as glass andplastics as described in greater detail below.

DETAILED DESCRIPTION

Aspects of the present disclosure include methods and systems forResonant Raman spectroscopy. Methods according to certain embodimentsinclude irradiating a sample with a monochromatic light source at afirst irradiation intensity and a second irradiation intensity,determining the intensity of one or more of the Resonant Ramanscattering and the intensity of fluorescence scattering at the firstirradiation intensity and second irradiation intensity, calculating arate of change of one or more of the intensity of Resonant Ramanscattering and the intensity of fluorescence scattering in response tothe change in irradiation intensity from the first irradiation intensityto the second irradiation intensity and comparing one or more of therate of change in the intensity of Resonant Raman scattering and therate of change in the intensity of fluorescence scattering with the rateof change in the irradiation intensity by the monochromatic light sourceto determine the spectroscopic response of the sample. Methods alsoinclude determining the presence or absence of a microorganism in asample and correcting for variations associated with measurementinstrumentation (e.g., monochromatic light source) and variationsassociated with the sample (e.g., fluorescence from non-targetcompounds). Also provided are methods for determining the antimicrobialsusceptibility of a microorganism to an antimicrobial agent as well asmethods for characterizing a phenotype of an unknown microorganism in asample. Systems for practicing the subject methods are also provided.

Before the present invention is described in greater detail, it is to beunderstood that this invention is not limited to particular embodimentsdescribed, as such may vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting, since the scope ofthe present invention will be limited only by the appended claims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range, is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges and are also encompassed within the invention, subject toany specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either orboth of those included limits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present invention, representativeillustrative methods and materials are now described.

All publications and patents cited in this specification are hereinincorporated by reference as if each individual publication or patentwere specifically and individually indicated to be incorporated byreference and are incorporated herein by reference to disclose anddescribe the methods and/or materials in connection with which thepublications are cited. The citation of any publication is for itsdisclosure prior to the filing date and should not be construed as anadmission that the present invention is not entitled to antedate suchpublication. Further, the dates of publication provided may be differentfrom the actual publication dates which may need to be independentlyconfirmed.

It is noted that, as used herein and in the appended claims, thesingular forms “a”, “an”, and “the” include plural referents unless thecontext clearly dictates otherwise. It is further noted that the claimsmay be drafted to exclude any optional element. As such, this statementis intended to serve as antecedent basis for use of such exclusiveterminology as “solely,” “only” and the like in connection with therecitation of claim elements, or use of a “negative” limitation.

As will be apparent to those of skill in the art upon reading thisdisclosure, each of the individual embodiments described and illustratedherein has discrete components and features which may be readilyseparated from or combined with the features of any of the other severalembodiments without departing from the scope or spirit of the presentinvention. Any recited method can be carried out in the order of eventsrecited or in any other order which is logically possible.

Resonant Raman Spectroscopy

As summarized above, aspects of the present disclosure include methodsfor Resonant Raman spectroscopy. Methods according to certainembodiments include irradiating a sample with a monochromatic lightsource at a first irradiation intensity and a second irradiationintensity, determining the intensity of one or more of the ResonantRaman scattering and the intensity of fluorescence scattering at thefirst irradiation intensity and second irradiation intensity,calculating a rate of change of one or more of the intensity of ResonantRaman scattering and the intensity of fluorescence scattering inresponse to the change in irradiation intensity from the firstirradiation intensity to the second irradiation intensity and comparingone or more of the rate of change in the intensity of Resonant Ramanscattering and the rate of change in the intensity of fluorescencescattering with the rate of change in the irradiation intensity by themonochromatic light source to determine the spectroscopic response ofthe sample.

In practicing methods according to certain embodiments, a sample isirradiated with a monochromatic light source. The term “monochromatic”is used herein in its conventional sense to refer to a light source thatoutputs a narrow bandwidth of light irradiation. In embodiments, themonochromatic light source outputs light having a narrow range ofwavelengths, such as a range of 25 nm or less, such as 20 nm or less,such as 15 nm or less, such as 10 nm or less, such as 5 nm or less andincluding 2 nm or less. In certain embodiments, the monochromatic lightsource outputs a single wavelength of light (e.g., 532 nm light). Anyconvenient monochromatic light source may be employed, such as a laseror a single wavelength light emitting diode. In certain embodiments, thelight source is a broadband light source in optical communication withan optical adjustment component that narrows the irradiation bandwidthto a single wavelength. For example, monochromatic light irradiation ofthe sample for Resonant Raman spectroscopy according to the subjectmethods may be achieved using a broadband light source such as abroadband halogen lamp, deuterium arc lamp, xenon arc lamp, stabilizedfiber-coupled broadband light source, a broadband LED with continuousspectrum, superluminescent emitting diode, semiconductor light emittingdiode, wide spectrum LED white light source or a multi-LED integratedwhite light source coupled to one or more optical bandpass filters,diffraction gratings, monochromators or any combination thereof.

In certain embodiments, the sample is irradiated with a laser. In someinstances, the laser is a continuous wave laser. In other instances, thelaser is a pulsed laser. In certain instances, the laser is a diodelaser, such as an ultraviolet diode laser, a visible diode laser and anear-infrared diode laser. In some instances, the monochromatic lightsource is a diode laser that outputs light at a wavelength from 375 nmto 1000 nm, such as from 405 nm to 875 nm, such as from 450 nm to 800nm, such as from 500 nm to 650 nm and including from 525 nm to 625 nm.In other instances, the laser is a pulsed laser, such as a solid statelaser. In certain instances, the monochromatic light source is asolid-state laser that outputs light at a wavelength from 375 nm to 1000nm, such as from 405 nm to 875 nm, such as from 450 nm to 800 nm, suchas from 500 nm to 650 nm and including from 525 nm to 625 nm. Othersuitable lasers may include, but are not limited to, helium-neon (HeNe)lasers, argon lasers, krypton lasers, xenon ion lasers, nitrogen lasers,carbon dioxide lasers, carbon monoxide lasers, excimer lasers, hydrogenfluoride lasers, deuterium fluoride lasers, oxygen-iodine lasers,gas-phase iodine lasers, helium cadium lasers, helium mercury lasers,helium silver lasers, strontium vapor lasers, neon copper lasers, coppervapor laser, gold vapor laser, manganese vapor lasers, ruby lasers,Nd:YAG lasers, NdCrYAG lasers, Er:YAG lasers, Nd:YLF lasers, Nd:YVO₄lasers, Nd:YCa₄O(BO₃)₃ lasers, Nd:glass lasers, titanium sapphirelasers, thulium YAG lasers, ytterbium YAG lasers, Yb₂O₃ lasers,ytterbium doped glass lasers, holmium YAG lasers, chromium ZnSe lasers,cerium doped lithium strontium aluminum fluoride lasers, promethium 147doped phosphate glass lasers, chromium doped chrysoberyl lasers, erbiumdoped and erbium-ytterbium codoped glass lasers, trivalent uranium dopedcalcium fluoride lasers, samarium doped calcium fluoride lasers, GaNlasers, InGaN lasers, AlGaInP lasers, AlGaAs lasers, InGaAsP lasers,among other laser types. In certain embodiments, the monochromatic lightsource is a frequency doubled neodymium-doped yttrium aluminium garnetthat outputs light at 532 nm.

In some embodiments, the sample is irradiated continuously. In otherembodiments, the sample is irradiated by the monochromatic light sourcein discrete intervals, such as for 0.001 milliseconds or more, such asfor 0.005 milliseconds or more, such as for 0.01 milliseconds or more,such as for 0.05 milliseconds or more, such as for 0.1 milliseconds ormore, such as for 0.5 milliseconds or more, such as for 1 millisecond ormore, such as for 5 milliseconds or more, such as for 10 milliseconds ormore, such as for 100 milliseconds or more, such as for 1000milliseconds or more, such as for 5 seconds or more, such as from 15seconds or more, such as for 30 seconds or more, such as for 60 secondsor more, such as from 100 seconds or more, such as for 200 seconds ormore, such as for 300 seconds or more, such as for 400 seconds or more,such as for 500 seconds or more, such as for 1000 seconds or more andincluding for 1500 seconds or more, or some other interval. The timebetween each interval may vary, and may be 0.001 milliseconds or more,such as 0.005 milliseconds or more, such as 0.01 milliseconds or more,such as 0.05 milliseconds or more, such as 0.1 milliseconds or more,such as 0.5 milliseconds or more, such as 1 millisecond or more, such as5 milliseconds or more, such as 10 milliseconds or more, such as 100milliseconds or more and including 1000 milliseconds or more.

In certain embodiments, the monochromatic light source is a stroboscopiclight source where the sample is illuminated with periodic flashes oflight. For example, the frequency of light strobe may be 0.01 kHz orgreater, such as 0.05 kHz or greater, such as 0.1 kHz or greater, suchas 0.5 kHz or greater, such as 1 kHz or greater, such as 2.5 kHz orgreater, such as 5 kHz or greater, such as 10 kHz or greater, such as 25kHz or greater, such as 50 kHz or greater and including 100 kHz orgreater.

The sample may be irradiated for any number of intervals to acquiresufficient Resonant Raman scattering and/or fluorescence scattering,such as irradiating the sample 1 time or more, such as 2 times or more,such as 3 times or more, such as 4 times or more, such as 5 times ormore, such as 10 times or more, such as 25 times or more and including50 times or more.

Depending on the type of light source, the optical components (e.g.,lens, mirrors, collimators, etc.), the sample may be irradiated by themonochromatic light source from any suitable distance, such as at adistance that is 1 mm or more from the sample, such as 2.5 mm or more,such as 5 mm or more, such as 10 mm or more, such as 15 mm or more, suchas 25 mm or more, such as 50 mm or more, such as 100 mm or more, such as500 mm or more, such as 1000 mm or more, such as 2500 mm or more, suchas 5000 mm or more and including 10000 mm or more from the sample.Likewise, the sample may be irradiated by the monochromatic light sourcefrom any suitable angle, such as from 5° to 90°, such as from 15° to85°, such as from 20° to 80°, such as from 25° to 75° and including from30° to 60°.

As summarized above, methods include determining the intensity of one ormore of Resonant Raman scattering and fluorescence scattering at one ormore wavenumbers. Resonant Raman scattering may be detected at anysuitable wavenumber depending on the chromophore, ranging from 200 cm⁻¹to 2000 cm⁻¹, such as from 250 cm⁻¹ to 1900 cm⁻¹, such as from 300 cm⁻¹to 1800 cm⁻¹, such as from 350 cm⁻¹ to 1700 cm⁻¹ and including from 400nm to 1600 cm⁻¹. In certain embodiments, the chromophore is lycopene andResonant Raman scattering is detected and measured at one or more of1512 cm⁻¹, 1515 cm⁻¹, 1525 cm⁻¹ and 1535 cm⁻¹. In other embodiments,methods also include detecting fluorescence at one or more wavenumbers,ranging from 1500 cm⁻¹ to 4000 cm⁻¹, such as from 1750 cm⁻¹ to 3750cm⁻¹, such as from 2000 cm⁻¹ to 3500 cm⁻¹, including 3000 cm⁻¹.

The duration for detecting light from the sample (e.g., Resonant Ramanscattering, fluorescence) in accordance with the subject method (asdescribed in greater detail below) may range from 10 seconds to 2000seconds, such as from 30 seconds to 1750 seconds, such as from 45seconds to 1500 seconds, such as from 60 seconds to 1250 seconds, suchas from 120 seconds to 1000 seconds, such as from 200 seconds to 800seconds and including from 400 seconds to 600 seconds.

Light from the sample (e.g., Resonant Raman scattering, fluorescence)may be detected by any convenient detection protocol, including but notlimited to photosensors or photodetectors, such as active-pixel sensors(APSs), quadrant photodiodes, wedge detectors image sensors,charge-coupled devices (CCDs), intensified charge-coupled devices(ICCDs), light emitting diodes, photon counters, bolometers,pyroelectric detectors, photoresistors, photovoltaic cells, photodiodes,photomultiplier tubes, phototransistors, quantum dot photoconductors orphotodiodes and combinations thereof, among other photodetectors. Incertain embodiments, Light from the sample (e.g., Resonant Ramanscattering, fluorescence) is detected with one or more CCDs.

Spectroscopy (e.g., non-linear Resonant Raman spectroscopy, fluorescencespectroscopy) as described herein may be conducted while maintaining aconstant temperature, such as where the temperature during the subjectmethods changes by 5° C. or less, such as by 4.5° C. or less, such as by4° C. or less, such as by 3.5° C. or less, such as by 3° C. or less,such as by 2.5° C. or less, such as by 2° C. or less, such as by 1.5° C.or less, such as 1° C. or less, such as by 0.5° C. or less, such as by0.1° C. or less, such as by 0.05° C. or less, such as by 0.01° C. orless, such as by 0.005° C., such as by 0.001° C., such as by 0.0001° C.,such as by 0.00001° C. or less and including by 0.000001° C. or less.Temperature may be controlled by any convenient protocol, including, butnot limited to heat sinks, fans, exhaust pumps, vents, refrigeration,coolants, heat exchanges, Peltier or resistive heating elements and anycombination thereof, among other types of temperature control protocols.

In some embodiments, the sample is irradiated through one or moreoptical adjustment components. By “optical adjustment” is meant thatlight from the monochromatic light source is changed or adjusted beforebeing impinged onto the sample. For example, the optical adjustment maybe to change the profile of the light beam, the focus of the light beam,the direction of beam propagation or to collimate the light beam. Insome instances, optical adjustment includes collimating the light. Theterm “collimate” is used in its conventional sense to refer to theoptically adjusting the collinearity of light propagation or reducingdivergence by the light of from a common axis of propagation. In someinstances, collimating includes narrowing the spatial cross section of alight beam. In other instances, optical adjustment includes changing thedirection of the light beam, such as changing the propagation of thelight beam by 1° or more, such as by 5° or more, such as by 10° or more,such as by 15° or more, such as by 20° or more, such as by 25° or more,such as by 30° or more, such as by 45° or more, such as by 60° or more,such as by 75° or more and including changing the direction of lightpropagation by 90° or more. In yet other instances, optical adjustmentis a de-magnification protocol so as to decrease the dimensions of thelight (e.g., beam spot), such as decreasing the dimensions by 5% ormore, such as by 10% or more, such as by 25% or more, such as by 50% ormore and including decreasing the dimensions by 75% or more.

Optical adjustment components may be any convenient device or structurewhich provides the desired change to the light beam and may include, butis not limited to, lenses, mirrors, beam splitters, collimating optics(e.g., lenses), pinholes, slits, gratings, light refractors, and anycombinations thereof. The subject systems, as described in greaterdetail below, may include one or more optical adjustment components asneeded, such as two or more, such as three or more, such as four or moreand including five or more optical adjustment components.

In certain embodiments, light detection systems include a collimatorpositioned adjacent to the sample holder. The collimator may be anyconvenient collimating protocol, such as one or more mirrors or curvedlenses or a combination thereof. For example, the collimator is incertain instances a single collimating lens. In other instances, thecollimator is a collimating mirror. In yet other instances, thecollimator includes two lenses. In still other instances, the collimatorincludes a mirror and a lens. Where the collimator includes one or morelenses, the focal length of each collimating lens may vary, ranging from5 mm to 500 mm, such as from 6 mm to 475 mm, such as from 7 mm to 450mm, such as from 8 mm to 425 mm, such as from 9 mm to 400 mm, such asfrom 10 mm to 375 mm, such as from 12.5 mm to 350 mm and including afocal length ranging from 15 mm to 300 mm. In certain embodiments, thefocal length ranges from 400 mm to 500 mm, such as from 405 mm to 475mm, such as from 410 mm to 450 mm and including from 410 mm to 425 mm,such as 410 mm or 420 mm.

In embodiments, the sample is irradiated in a sample holder, e.g., asample container. The sample holder may be any suitable shaped substrateor container for irradiating a sample and detecting one or more ofResonant Raman scattering and fluorescence scattering. In someembodiments, the sample holder is a planar substrate (e.g., microscopeslide). In other embodiments, the sample holder is a microfluidic devicehaving one or more microfluidic channels. In yet other embodiments, thesample holder is a container having a cross-sectional shape, wherecross-sectional shapes of interest include, but are not limited to:rectilinear cross sectional shapes, e.g., squares, rectangles,trapezoids, triangles, hexagons, etc., curvilinear cross-sectionalshapes, e.g., circles, ovals, etc., as well as irregular shapes, e.g., aparabolic bottom portion coupled to a planar top portion, etc. The sizeof the sample holder may vary, depending on the volume of the samplesbeing irradiated, where holders of interest have a length that rangesfrom 5 mm to 100 mm, such as from 10 mm to 90 mm, such as from 15 mm to85 mm, such as from 20 mm to 80 mm, such as from 25 mm to 75 mm, such asfrom 30 mm to 70 mm and including from 35 mm to 65 mm and a width (orcross-section where the container is cylindrical) of from 5 mm to 100mm, such as from 10 mm to 90 mm, such as from 15 mm to 85 mm, such asfrom 20 mm to 80 mm, such as from 25 mm to 75 mm, such as from 30 mm to70 mm and including from 35 mm to 65 mm. In embodiments, the sampleholder may have a volume of from 0.1 cm³ to 10 cm³, such as from 0.5 cm³to 9 cm³, such as from 1 cm³ to 8 cm³, such as from 1.5 cm³ to 7 cm³,such as from 2 cm³ to 6 cm³, such as from 2.5 cm³ to 5 cm³ includingfrom 3 cm³ to 4 cm³.

The sample holder may be formed from any transparent material whichpasses the desired range of wavelength, including but not limited tooptical glass, borosilicate glass, Pyrex glass, ultraviolet quartz,infrared quartz, sapphire. In certain embodiments, the sample containeris glass having walls with a zwitterionic coating, such as azwitterionic silane coating (e.g., as described in the ExperimentalSection below). The sample container may also be formed from plastic,such as polycarbonates, polyvinyl chloride (PVC), polyurethanes,polyethers, polyamides, polyimides, or copolymers of thesethermoplastics, such as PETG (glycol-modified polyethyleneterephthalate), among other polymeric plastic materials, includingpolyester, where polyesters of interest may include, but are not limitedto poly(alkylene terephthalates) such as poly(ethylene terephthalate)(PET), bottle-grade PET (a copolymer made based on monoethylene glycol,terephthalic acid, and other comonomers such as isophthalic acid,cyclohexene dimethanol, etc.), poly(butylene terephthalate) (PBT), andpoly(hexamethylene terephthalate); poly(alkylene adipates) such aspoly(ethylene adipate), poly(1,4-butylene adipate), andpoly(hexamethylene adipate); poly(alkylene suberates) such aspoly(ethylene suberate); poly(alkylene sebacates) such as poly(ethylenesebacate); poly(ε-caprolactone) and poly(β-propiolactone); poly(alkyleneisophthalates) such as poly(ethylene isophthalate); poly(alkylene2,6-naphthalene-dicarboxylates) such as poly(ethylene2,6-naphthalene-dicarboxylate); poly(alkylene sulfonyl-4,4′-dibenzoates)such as poly(ethylene sulfonyl-4,4′-dibenzoate); poly(p-phenylenealkylene dicarboxylates) such as poly(p-phenylene ethylenedicarboxylates); poly(trans-1,4-cyclohexanediylalkylene dicarboxylates)such as poly(trans-1,4-cyclohexanediyl ethylene dicarboxylate);poly(1,4-cyclohexane-dimethylene alkylene dicarboxylates) such aspoly(1,4-cyclohexane-dimethylene ethylene dicarboxylate);poly([2.2.2]-bicyclooctane-1,4-dimethylene alkylene dicarboxylates) suchas poly([2.2.2]-bicyclooctane-1,4-dimethylene ethylene dicarboxylate);lactic acid polymers and copolymers such as (S)-polylactide,(R,S)-polylactide, poly(tetramethylglycolide), andpoly(lactide-co-glycolide); and polycarbonates of bisphenol A,3,3′-dimethylbisphenol A, 3,3′,5,5′-tetrachlorobisphenol A,3,3′,5,5′-tetramethylbisphenol A; polyamides such as poly(p-phenyleneterephthalamide); polyesters, e.g., polyethylene terephthalates, e.g.,Mylar™ polyethylene terephthalate; etc.

In embodiments, the sample holder may pass light that ranges from 100 nmto 1500 nm, such as from 150 nm to 1400 nm, such as from 200 nm to 1300nm, such as from 250 nm to 1200 nm, such as from 300 nm to 1100 nm, suchas from 350 nm to 1000 nm, such as from 400 nm to 900 nm and includingfrom 500 nm to 800 nm, for example 532 nm.

As summarized above, methods include irradiating the sample with amonochromatic light source at a first irradiation intensity and a secondirradiation intensity and determining the intensity of Resonant Ramanscattering at the first irradiation intensity and second irradiationintensity. To detect Resonant Raman scattering, samples of interest inthe subject methods include a compound which exhibits Resonant Ramanscattering in response to irradiation by a monochromatic light source.In some embodiments, the compound is a chromophore where the incidentirradiation frequency of the monochromatic light source is close inenergy to an electronic transition of the compound. For example, methodsinclude in certain instances, irradiating a sample with a monochromaticlight source having a frequency that is 100 cm⁻¹ or less from anelectronic transition of a chromophore in the sample, such as 90 cm⁻¹ orless, such as 80 cm⁻¹ or less, such as 70 cm⁻¹ or less, such as 60 cm⁻¹or less, such as 50 cm⁻¹ or less, such as 40 cm⁻¹ or less, such as 30cm⁻¹ or less, such as 25 cm⁻¹ or less, such as 20 cm⁻¹ or less, such as15 cm⁻¹ or less, such as 10 cm⁻¹ or less, such as 5 cm⁻¹ or less, suchas 4 cm⁻¹ or less, such as 3 cm⁻¹ or less, such as 2 cm⁻¹ or less, suchas 1 cm⁻¹ or less, such as 0.5 cm⁻¹ or less, such as 0.1 cm⁻¹ or less,such as 0.05 cm⁻¹ or less, such as 0.01 cm⁻¹ or less and includingirradiating with a monochromatic light source having a frequency that is0.001 cm⁻¹ or less from an electronic transition of a chromophore in thesample.

Depending on the wavelength of irradiation and the type of monochromaticlight source (e.g., laser), chromophores in samples of the subjectmethods may vary. In some embodiments, the chromophore is a hydrophobiccompound that exhibits Resonant Raman scattering in response to laserirradiation. In some instances, the chromophore is a carotene orcarotenoid. For example, Carotenoids of interest include, but are notlimited to, carotene (e.g., α-carotene, β-carotene, γ-carotene,δ-carotene, ε-carotene, lycopene, etc.) and xanthophylls (e.g., lutein,zeaxanthin, neoxanthin, violaxanthin, flavoxanthin, α- andβ-cryptoxanthin, etc.). In certain embodiments, the chromophore islycopene.

In some embodiments, the chromophore is associated with anothercomponent in the sample, such as to increase solubility of thechromophore in the sample. In certain instances, the chromophore ishydrophobic and is non-covalently associated with an albumin protein.Albumin proteins of interest include, but are not limited to, humanserum albumin (HSA; Gene ID: 213); bovine serum albumin (BSA; Gene ID:280717); mouse albumin (Gene ID: 11657); rat albumin (Gene ID: 24186);goat albumin (Gene ID: 100860821); donkey albumin (Gene ID: 106835108);horse albumin (Gene ID: 100034206); camel albumin (Gene ID: 105080389 or105091295), etc. or a protein having an amino acid sequence having atleast about 80%, at least about 85%, at least about 90%, at least about95%, at least about 98%, at least about 99%, or 100%, amino acidsequence identity to human serum albumin (HSA; Gene ID: 213); bovineserum albumin (BSA; Gene ID: 280717); mouse albumin (Gene ID: 11657);rat albumin (Gene ID: 24186); goat albumin (Gene ID: 100860821); donkeyalbumin (Gene ID: 106835108); horse albumin (Gene ID: 100034206); camelalbumin (Gene ID: 105080389 or 105091295).

In certain embodiments, samples of the present disclosure include ahydrophobic compound (e.g., chromophore) that is non-covalentlyassociated with an albumin protein, such as those described in the U.S.Patent Publication No. 2016/0324933, filed on May 6, 2016, thedisclosure of which is herein incorporated by reference in its entirety.

Samples of the subject methods may also include a free radicalscavenger. The term “free radical scavenger” is used herein in itsconventional sense to refer to a compound that reacts, complexes orotherwise removes free radicals in a composition. Free radicalscavengers of the subject methods may be antioxidants, oxygenscavengers, gas ion scavengers, hydroxyl radical scavengers and thelike. In certain embodiments, the free radical scavenger is bilirubin ora derivative thereof, such as unconjugated bilirubin that is not watersoluble at pH 7.2.

In some embodiments, the bilirubin or derivative thereof isnon-covalently associated with a protein, such as an albumin protein asdescribed above. The term “non-covalently” is used herein in itsconventional sense to refer to interactions between the bilirubin orderivative thereof with the protein and may include dipole-dipole bonds,van der Waals interaction, ionic bonding, ion-dipole bonds, hydrogenbonding, among other types of non-covalent bonding. In some instances,the bilirubin or derivative thereof is positioned at least partiallywithin the albumin protein. In certain instances, the bilirubin orderivative thereof is coupled to a binding site in the albumin protein.

The free radical scavenger may be present in the sample in an amountthat varies, ranging from 0.001 μM to 5 μM, such as from 0.005 μM to 4.9μM, such as from 0.01 μM to 4.8 μM, such as from 0.05 μM to 4.7 μM, suchas from 0.1 μM to 4.6 μM, such as from 0.5 μM to 4.5 μM, such as from0.75 μM to 4 μM and including from 0.75 μM to 1.5 μM, for example 0.75μM to 1.25 μM. In certain instances, the free radical scavenger isbilirubin or a derivative thereof and is present in the sample in anamount of from 0.001 μM to 5 μM, such as from 0.005 μM to 4.9 μM, suchas from 0.01 μM to 4.8 μM, such as from 0.05 μM to 4.7 μM, such as from0.1 μM to 4.6 μM, such as from 0.5 μM to 4.5 μM, such as from 0.75 μM to4 μM and including from 0.75 μM to 1.5 μM, for example 0.75 μM to 1.25μM.

In some embodiments, samples include a reducing agent. The term“reducing agent” is used herein in its conventional sense to refer to acompound that loses (“or donates”) an electron to another chemicalspecies in a redox chemical reaction. In certain embodiments, thereducing agent is glutathione or a derivative thereof.

The reducing agent may be present in the sample in an amount thatvaries, ranging from 0.001 mg/mL to 10 mg/mL, such as from 0.005 mg/mLto 9 mg/mL, such as from 0.01 mg/mL to 8 mg/mL, such as from 0.05 mg/mLto 7 mg/mL, such as from 0.1 mg/mL to 6 mg/mL, for example from 0.1mg/mL to 1 mg/mL. In certain instances, the reducing agent isglutathione or a derivative thereof and is present in the sample in anamount of from 0.001 mg/mL to 10 mg/mL, such as from 0.005 mg/mL to 9mg/mL, such as from 0.01 mg/mL to 8 mg/mL, such as from 0.05 mg/mL to 7mg/mL, such as from 0.1 mg/mL to 6 mg/mL, for example from 0.1 mg/mL to1 mg/mL.

In some embodiments, samples include a crosslinking agent. In someinstances, the crosslinking agent may be a disulfide crosslinker (e.g.,a compound having disulfide linkages that exchanges disulfide bonds witha cysteine groups on proteins). In some instances, the crosslinkingagent has a core that is a glutamic acid derivative, such as a glutamicacid derivative having one or more disulfide linkages. In certainembodiments, the crosslinking agent is a compound of Formula (I):

where:

R₁, and R₂ are independently selected from hydrogen, alkyl, substitutedalkyl, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl,heteroalkyl, substituted heteroalkyl, heterocycloalkyl, substitutedheterocycloalkyl, heteroaryl and substituted heteroaryl;

X₁ and X₂ are independently selected from N, O, or S; and

R₃ is a hydrogen, alkyl, substituted alkyl, amino, halogen, cyano,alcohol or alkoxy.

In some embodiments, R₁, and R₂ are heteroaryl, X₁ and X₂ are N and R₃is amino.

In certain embodiments, the crosslinking agent is a compound of Formula(DS-1)

The crosslinking agent may be present in the sample in an amount wherethe molar ratio of crosslinking agent to albumin protein is from 1:10 to10:1, such as from 1:9 to 9:1, such as from 1:8 to 8:1, such as from 1:7to 7:1, such as from 1:6 to 6:1, such as from 1:5 to 5:1, such as from1:4 to 4:1, such as from 1:3 to 3:1, and including from 1:2 to 2:1. Incertain embodiments, the molar ratio of crosslinking agent to albuminprotein in samples of the subject methods is about 1:2. According tocertain embodiments, methods include irradiating the sample over aplurality of intensities by the monochromatic light source over a periodof time and determining a rate of change in the intensity of one or moreof the Raman scattering and fluorescence scattering. The sample may beirradiated in these embodiments for any desired duration, such as from10 seconds to 1500 seconds, such as from 30 seconds to 1400 seconds,such as from 45 seconds to 1300 seconds, such as from 60 seconds to 1200seconds, such as from 120 seconds to 1000 seconds, such as from 200seconds to 800 seconds and including from 400 seconds to 600 seconds. Insome embodiments, a normalized rate of change of the intensity ofResonant Raman scattering is calculated. In other embodiments, anormalized rate of change of irradiation intensity by the monochromaticlight source (e.g., laser) is also calculated.

In certain embodiments, methods include irradiating the sample at aninterface (e.g., by focusing the monochromatic light source with acollimator as described above) between the sample and a surface of thesample holder (e.g., wall of the sample container). By “interface” ismeant the space where the surface of the sample holder (e.g., containerwall) comes into contact with the sample. In embodiments, the interfaceirradiated by the monochromatic light source in the subject methods mayextend from about 0.01 mm to 2 mm from the surface of the container wall(i.e., where the sample comes into contact with the container), such asfrom 0.02 mm to 1.9 mm, such as from 0.03 mm to 1.8 mm, such as from0.04 mm to 1.7 mm, such as from 0.05 mm to 1.6 mm, such as from 0.06 mmto 1.5 mm, such as from 0.07 mm to 1.4 mm, such as from 0.08 mm to 1.3mm, such as from 0.09 mm to 1.2 mm, such as from 0.1 mm to 1 mm, forexample 0.2 mm from the surface of the sample holder (e.g., containerwall). In these embodiments, the sample holder (e.g., glass vial) ismaintained substantially at rest (e.g., no vibration, agitation, etc.)and the velocity of the interfacial liquid layer irradiated by themonochromatic light source is near or at zero. For example, the liquidvelocity of the interfacial sample layer irradiated by the monochromaticlight source may be 10⁻² cm³/second or less, such as 10⁻³ cm³/second orless, such as 10⁻⁴ cm³/second or less, such as 10⁻⁵ cm³/second, such as10⁻⁶ cm³/second, such as 10⁻⁷ cm³/second or less, such as 10⁻⁸cm³/second or less, such as 10⁻⁹ cm³/second or less and including 10⁻¹⁰cm³/second or less. In certain embodiments, the velocity of the sampleat the interfacial layer irradiated by the monochromatic light source inthe subject methods is zero cm³/second.

Methods also include determining the spectroscopic response of a sampleby calculating a rate of change of the intensity of one or more of theResonant Raman scattering and fluorescence scattering in response to thechange in irradiation intensity from the first irradiation intensity tothe second irradiation intensity and comparing the rate of change in theintensity of one or more of the Resonant Raman scattering andfluorescence scattering with the rate of change in the irradiationintensity by the monochromatic light source. In some embodiments, thespectroscopic response of the sample is indicative of a physical changeover time in the sample. In other embodiments, the spectroscopicresponse of the sample is indicative of a chemical change over time inthe sample. In still other embodiments, the spectroscopic response ofthe sample is indicative of the presence of an actively metabolizingmicroorganism in the sample.

In embodiments, methods include irradiating the sample over a pluralityof intensities by the monochromatic light source over a period of timeand determining a rate of change in the intensity of one or more of theResonant Raman scattering and fluorescence scattering and comparing therate of change in the intensity of one or more of the Resonant Ramanscattering and fluorescence scattering with the rate of change in thenormalized irradiation intensity by the monochromatic light source todetermine a net signal. In calculating the net signal, methods mayfurther include calculating a normalized rate of change of the intensityof one or more of the Resonant Raman scattering and fluorescencescattering and a normalized rate of change of irradiation intensity andcomparing the normalized rate of change of the intensity of one or moreof the Resonant Raman scattering and fluorescence scattering to thenormalized rate of change of irradiation intensity to determine the netsignal.

In embodiments of the present disclosure, the term “normalized” is usedherein in its conventional sense to refer to adjusting values measuredon different scales to a notionally common scale. For example,normalized values may provide for the comparison of correspondingnormalized values for different datasets which eliminates the effect ofgross influences. In certain embodiments, determining the normalizedrate of change includes dividing the slope (e.g., of the linear fit ofthe dataset) with the absolute value observed at time=0.

The range of normalized irradiation intensity may vary depending on thechromophore and the monochromatic light source. In some embodiments, themonochromatic light source is a laser and the normalized intensity ofthe laser is varied by 10% or more, such as by 15% or more, such as by25% or more, such as by 50% or more, such as by 75% or more, such as by90% or more and including by 99% or more. In these embodiments, thenormalized rate of change of the laser intensity may vary, ranging from−10×10⁻⁵ sec⁻¹ to 10×10⁻⁵ sec⁻¹, such as from −9×10⁻⁵ sec⁻¹ to 9×10⁻⁵sec⁻¹, such as from −8×10⁻⁵ sec⁻¹ to 8×10⁻⁵ sec⁻¹, such as from −7×10⁻⁵sec⁻¹ to 7×10⁻⁵ sec⁻¹, such as from −6×10⁻⁵ sec⁻¹ to 6×10⁻⁵ sec⁻¹, suchas from −5×10⁻⁵ sec⁻¹ to 5×10⁻⁵ sec⁻¹, such as from −4×10⁻⁵ sec⁻¹ to4×10⁻⁵ sec⁻¹, such as from −3×10⁻⁵ sec⁻¹ to 3×10⁻⁵ sec⁻¹, such as from−2×10⁻⁵ sec⁻¹ to 2×10⁻⁵ sec⁻¹ and including from −1×10⁻⁵ sec⁻¹ to 1×10⁻⁵sec⁻¹. The normalized rate of change in the intensity of Resonant Ramanscattering may also vary, ranging from −10×10⁻⁵ sec⁻¹ to 10×10⁻⁵ sec⁻¹,such as from −9×10⁻⁵ sec⁻¹ to 9×10⁻⁵ sec⁻¹, such as from −8×10⁻⁵ sec⁻¹to 8×10⁻⁵ sec⁻¹, such as from −7×10⁻⁵ sec⁻¹ to 7×10⁻⁵ sec⁻¹, such asfrom −6×10⁻⁵ sec⁻¹ to 6×10⁻⁵ sec⁻¹, such as from −5×10⁻⁵ sec⁻¹ to 5×10⁻⁵sec⁻¹, such as from −4×10⁻⁵ sec⁻¹ to 4×10⁻⁵ sec⁻¹, such as from −3×10⁻⁵sec⁻¹ to 3×10⁻⁵ sec⁻¹, such as from −2×10⁻⁵ sec⁻¹ to 2×10⁻⁵ sec⁻¹ andincluding from −1×10⁻⁵ sec⁻¹ to 1×10⁻⁵ sec⁻¹.

Methods according to certain embodiments include characterizing a samplecomposition with the net signal. For example, the net signal may be usedto detect a change in a sample composition or for determining whethertwo compositions have equivalent or different makeup. In certainembodiments, the net signal is used to characterize the amount of gasespresent in the sample. In other embodiments, the net signal may be usedto determine if actively metabolizing microorganisms are present in asample.

In one embodiment, methods include irradiating a first sample over aplurality of intensities by the monochromatic light source (e.g., laser)for a period of time and determining a first rate of change in theintensity of one or more of Raman scattering and fluorescencescattering; irradiating a second sample over a plurality of intensitiesby the monochromatic light source for the period of time and determininga rate of change in the intensity of one or more of Raman scattering andfluorescence scattering for the second sample. The net signal the firstsample is calculated by comparing the normalized rate of change in theintensity of one or more of Resonant Raman scattering and fluorescencescattering with the normalized rate of change in the irradiationintensity of the first sample by the monochromatic light source. The netsignal of the second sample is determined by comparing the normalizedrate of change in the intensity of one or more of Resonant Ramanscattering and fluorescence scattering with the normalized rate ofchange in the irradiation intensity of the second sample by themonochromatic light source.

In some embodiments, the net signal of the first sample and the netsignal of the second sample are the same. In other embodiments, the netsignal of the first sample and the net signal of the second sample aredifferent. In some instances, this difference is indicative that theamount of gases (e.g., carbon dioxide, oxygen, methane, nitrogen, etc.)present in the first sample and the second sample is different. In otherinstances, this difference is indicative that the type of gases presentin the first sample and the second sample is different. In yet otherinstances, a difference between the first net signal and the second netsignal is indicative that the amount of solubilized gases (i.e., gasdissolved into the sample solution) is different.

Methods of Determining the Presence of a Microorganism in a Sample byResonant Raman Scattering

Aspects of the present disclosure also include determining the presenceof a microorganism (e.g., an actively metabolizing microorganism) in asample by Resonant Raman scattering. Methods according to certainembodiments include irradiating a sample over a plurality of intensitiesby a monochromatic light source for a period of time and calculating arate of change in the intensity of Resonant Raman scattering for thefirst sample; calculating a net signal of the sample by comparing anormalized rate of change in the intensity of Resonant Raman scatteringfor the sample with a normalized rate of change in the irradiationintensity of the sample by the monochromatic light source; anddetermining the presence of a microorganism in the sample based on thenet signal of the sample.

Methods according to certain embodiments, include combining in a sampleholder the sample with a reagent that contains albumin with anincorporated ligand; irradiating the sample with a monochromatic lightsource that is absorbed by the ligand, with either an invariant lightintensity or one that varies over time focused at an interface betweenthe sample and a surface of the sample holder; collecting scatteredlight from the irradiated sample and measuring a Raman signal and afluorescence signal from the scattered light at a plurality of differenttimes; calculating a rate of change in intensity of the Raman signal andfluorescence signal for the sample over time; correcting the calculatedrates of change in the intensities of the Raman signal and thefluorescence signal to obtain a net signal; and determining the presenceof a microorganism in the sample based on a comparison of the net signalversus one or more preset thresholds.

In some instances, correcting the rate of change in the intensities ofthe Raman signal and the fluorescence signal includes characterizing aspectral output from a standard sample. In other instances, correctingthe rate of change in the intensities of the Raman signal includescharacterizing a fluorescence output from the reagent.

In certain embodiments, correcting the rate of change in the intensitiesof the Raman signal and the fluorescence signal includes determining arate of change in total output from a standard reference sample andcalculating a net signal as the rate of change in the intensity of theResonant Raman scattering minus the rate of change in the intensity ofResonant Raman scattering from the standard sample.

In other embodiments, correcting the rate of change in the intensitiesof the Raman signal and the fluorescence signal includes determining arate of change in the intensity of fluorescent scattering from astandard reference sample and calculating a net signal as the rate ofchange in the intensity of the Resonant Raman scattering minus the rateof change in the intensity of fluorescent scattering from the standardsample.

In certain embodiments, a microorganism is determined to be present whenthe net signal of the sample is above a predetermined threshold.Depending on the chromophore in the sample (e.g., lycopenenon-covalently associated with albumin) and the microorganism, thethreshold may vary, ranging from −0.5 to −4×10⁻⁵/sec, such as from −0.5to −1.0×10⁻⁵/sec, such as from −1 to −2×10⁻⁵/sec and including apredetermined threshold where the net signal is 1. In some embodiments,the one or more present thresholds are set by implementing the methodabove on one or more control samples that contains an inoculum in anamount at a lower limit of concentration in a clinically infectedsample. In some embodiments, a microorganism is determined to be presentin the sample when the net signal of the sample exceeds the threshold by1% or more of the threshold value, such as 5% or more, such as 10% ormore, such as 15% or more, such as 25% or more, such as 50% or more,such as 75% or more and including 90% or more. In certain instances, amicroorganism is determined to be present in the sample when the netsignal of the sample exceeds the threshold by 2-fold or more, such as3-fold or more, such as 5-fold or more and including 10-fold or more.

In other embodiments, determining the presence of a microorganismincludes comparing the net signal of two different samples. In someembodiments, one of the samples is a reference sample that does notcontain a microorganism. In these embodiments, methods may includeincludes: irradiating a first sample over a plurality of intensities bya monochromatic light source for a period of time and calculating a rateof change in the intensity of Resonant Raman scattering for the firstsample; calculating a net signal of the first sample by comparing anormalized rate of change in the intensity of Resonant Raman scatteringfor the first sample with a normalized rate of change in the irradiationintensity of the first sample by the monochromatic light source;irradiating a second sample over a plurality of intensities by themonochromatic light source for the period of time and determining a rateof change in the intensity of Resonant Raman scattering for the secondsample; calculating a net signal of the second sample by comparing anormalized rate of change in the intensity of Resonant Raman scatteringfor the second sample with a normalized rate of change in theirradiation intensity of the second sample by the monochromatic lightsource; and determining the presence of a microorganism in one or moreof the first sample or the second sample by comparing the net signal ofthe first sample with the net signal of the second sample.

In some instances, a microorganism is determined to be present in thesecond sample when the net signal of the second sample is greater thanthe net signal of the first sample. In other instances, a microorganismis determined to be present in the first sample when the net signal ofthe first sample is greater than the net signal of the second sample.Where the first sample is a reference sample, a microorganism isdetermined to be present in the second sample when the net signal of thesecond sample is greater than the net signal of the reference sample.

Methods of Determining the Presence of a Microorganism in a Sample byFluorescence

Aspects of the present disclosure also include determining the presenceof a microorganism (e.g., an actively metabolizing microorganism) in asample by fluorescence. Methods according to certain embodiments includeirradiating a sample by a monochromatic light source for a period oftime and detecting fluorescence from the sample over the period of time;calculating a rate of change of the fluorescence due to the presence ofa microorganism by comparing a normalized rate of change in theintensity of the detected fluorescence produced by the sample with anormalized rate of change of fluorescence produced by a control; anddetermining the presence of a microorganism in the sample based on thecalculated changes in the fluorescence of the sample compared to presetthresholds.

In some embodiments, the sample is irradiated over a plurality ofintensities by the monochromatic light source. The fluorescence producedby the sample and the control is detected from 2500 cm⁻¹ to 3500 cm⁻¹,such as at 3000 cm⁻¹. In embodiments, the control and sample include areagent composition that includes a hydrophobic compound non-covalentlyassociated with an albumin protein. The control sample is, in someinstances, a composition that includes the reagent composition and doesnot include a microorganism. For example, the control is a compositionthat has the same components as the sample in the absence ofmicroorganism. In some embodiments, the control includes only thecomponents of the reagent composition. In other embodiments, the controlincludes the components of the reagent composition andmicroorganism-free plasma.

Methods of Calculating Signal-to-Noise Ratio

Aspects of the present disclosure also include methods for calculatingsignal-to-noise ratio in non-linear Resonant Raman spectroscopy. In someembodiments, the signal-to-noise ratio is calculated by: irradiating afirst sample over a plurality of intensities by a monochromatic lightsource for a period of time and determining a rate of change in theintensity of Resonant Raman scattering for the first sample; calculatingan average rate of change in the intensity of Resonant Raman scatteringby the first sample to give a first average rate of change; calculatinga standard deviation for the first average rate of change; irradiating asecond sample over a range of intensities by the monochromatic lightsource for the period of time and determining a rate of change in theintensity of Resonant Raman scattering for the second sample;calculating an average rate of change in the intensity of Resonant Ramanscattering by the second sample to give a second average rate of change;calculating a standard deviation for the second average rate of change;subtracting the second average rate of change from the first averagerate of change to give a signal average rate of change; adding the firststandard deviation and the second standard deviation to give a signalstandard deviation; and dividing the signal average rate of change bythe signal standard deviation to determine a signal-to-noise ratio forResonant Raman response.

In some embodiments, the first sample includes a hydrophobic compoundnon-covalently associated with an albumin protein and the second sampleincludes a hydrophobic compound non-covalently associated with analbumin protein and a microorganism. For example, the first sample mayinclude lycopene non-covalently associated with an albumin protein andthe second sample includes lycopene non-covalently associated with analbumin protein and a microorganism.

In certain embodiments, methods include enhancing the signal-to-noiseratio by contacting the first sample and the second sample with a freeradical scavenger, such as bilirubin or a derivative thereof. In certainembodiments, the free radical scavenger (e.g., bilirubin or derivativethereof) enhances the signal-to-noise ratio by 5% or greater, such as by10% or greater, such as by 15% or greater, such as by 25% or greater,such as by 50% or greater, such as by 75% or greater, such as by 90% orgreater, such as by 95% or greater, such as by 1.5-fold or greater, suchas by 2-fold or greater, such as by 3-fold or greater, such as by 5-foldor greater and including by 10-fold or greater.

The free radical scavenger may be present in these embodiments in anamount that varies, ranging from 0.001 μM to 5 μM, such as from 0.005 μMto 4.9 μM, such as from 0.01 μM to 4.8 μM, such as from 0.05 μM to 4.7μM, such as from 0.1 μM to 4.6 μM, such as from 0.5 μM to 4.5 μM, suchas from 0.75 μM to 4 μM and including from 0.75 μM to 1.5 μM, forexample 0.75 μM to 1.25 μM. In certain instances, bilirubin or aderivative thereof is contacted with the first sample and second samplein an amount of from 0.001 μM to 5 μM, such as from 0.005 μM to 4.9 μM,such as from 0.01 μM to 4.8 μM, such as from 0.05 μM to 4.7 μM, such asfrom 0.1 μM to 4.6 μM, such as from 0.5 μM to 4.5 μM, such as from 0.75μM to 4 μM and including from 0.75 μM to 1.5 μM, for example 0.75 μM to1.25 μM.

Depending on the amount of free radical scavenger (e.g., bilirubin orderivative thereof), the duration for irradiating the first and secondsamples varies, such as from 10 seconds to 2000 seconds, such as from 30seconds to 1750 seconds, such as from 45 seconds to 1500 seconds, suchas from 60 seconds to 1250 seconds, such as from 120 seconds to 1000seconds, such as from 200 seconds to 800 seconds and including from 400seconds to 600 seconds. In some embodiments, the free radical scavenger(e.g., bilirubin or a derivative thereof) is present in the first sampleand the second sample in an amount that ranges from 0.75 μM to about1.25 μM and the first sample and the second sample are irradiated for aduration of from 600 seconds to 900 seconds. In one example, the freeradical scavenger (e.g., bilirubin or a derivative thereof) is presentin the first sample and the second sample in an amount of about 1 μM,and the first sample and the second sample are irradiated for a durationof from 600 seconds to 900 seconds. In another example, the free radicalscavenger (e.g., bilirubin or a derivative thereof) is present in thefirst sample and the second sample in an amount of about 1.5 μM, and thefirst sample and the second sample are irradiated for a duration of from900 seconds to 1200 seconds.

Methods for Correcting for Thermal Drift

Aspects of the present disclosure also include methods for correctingfor thermal drift in the monochromatic light source in non-linearResonant Raman spectroscopy. In some embodiments, the monochromaticlight source is a laser and the subject methods correct for thermaldrift of the laser in non-linear Resonant Raman spectroscopy.

In certain embodiments, methods include first determining whether themonochromatic light source exhibits thermal drift. In these embodiments,methods include: irradiating a reference composition over a plurality ofintensities by the monochromatic light source for the period of time anddetermining a rate of change in the intensity of Resonant Ramanscattering, wherein the reference composition comprises a referencecompound that exhibits no change in the intensity of Resonant Ramanscattering in response to the change in irradiation intensity by themonochromatic light source; and determining a net signal of thereference composition by comparing the rate of change in the intensityof Resonant Raman scattering for the reference composition with the rateof change in the irradiation intensity of the reference composition bythe monochromatic light source to determine if the monochromatic lightsource exhibits thermal drift.

In these embodiments, the reference composition includes a referencecompound that exhibits no change in the intensity of Resonant Ramanscattering in response to the change in irradiation intensity, such asthe NIST calibration standard SRM 2242.

Methods may also include correcting for the thermal drift in themonochromatic light source. To correct for laser drift, methods mayinclude irradiating a sample over a plurality of intensities by amonochromatic light source for a period of time and determining a rateof change in the intensity of Resonant Raman scattering; determining therate of change of the output from the reference composition to produce acorrection factor; and subtracting the correction factor from thedetermined rate of change in the intensity of Resonant Raman scatteringfor the sample to correct for the thermal drift of the monochromaticlight source.

Methods for Characterizing the Susceptibility of a Microorganism to anAntimicrobial Agent with Resonant Raman Scattering

Aspects of the present disclosure also include methods for determiningthe susceptibility of a microorganism to an antimicrobial agent withResonant Raman scattering. In some embodiments, methods includedetermining the minimum inhibitory concentration (MIC) of theantimicrobial agent (i.e., the lowest concentration of antimicrobialagent that inhibits growth of the microorganism). In other embodiments,methods include determining the minimum bactericidal concentration (MBC)of the antimicrobial agent (i.e., the lowest concentration ofantimicrobial agent required to kill the microorganism)

In embodiments, methods include irradiating a plurality of samples, eachsample comprising a microorganism and an antimicrobial agent over aplurality of intensities by the monochromatic light source for a periodof time and determining a rate of change in the intensity of ResonantRaman scattering for each irradiated sample, wherein each samplecomprises the same concentration of microorganism and differentconcentrations of antimicrobial agent; determining a net signal for eachsample by comparing a normalized rate of change in the intensity ofResonant Raman scattering for each sample with a normalized rate ofchange in the irradiation intensity of each sample by the monochromaticlight source; and determining the susceptibility of the microorganism tothe antimicrobial agent based on the net signal for the plurality ofsamples.

In some embodiments, methods further include comparing the net signalfor each sample. For example, comparing the net signal for each samplemay include plotting the net signal for each sample as a function of thelog of the concentration of antimicrobial agent in each sample. In theseembodiments, methods may further include determining one or more of theconcentration of antimicrobial agent that exhibits a decrease in the netsignal and the concentration of antimicrobial agent that exhibits anincrease in the net signal. In some embodiments, the concentration ofantimicrobial agent that first exhibits a decrease in the net signal onthe plot is determined to be the minimum inhibitory concentration (MIC)of the antimicrobial agent for the microorganism. In other embodiments,the concentration of antimicrobial agent that exhibits an increase inthe net signal on the plot is determined to be the minimum bactericidalconcentration (MBC) of the antimicrobial agent for the microorganism. Insome embodiments, methods include determining metabolic activity of themicroorganism in each sample based on the net signal for each sample.For example, methods may include determining the concentration ofantimicrobial agent that exhibits a decrease in metabolic activity ordetermining the concentration of antimicrobial agent that exhibits anincrease in the metabolic activity. In these embodiments, the minimuminhibitory concentration of the antimicrobial agent may be determined tobe the concentration of antimicrobial agent that exhibits a decrease inmetabolic activity of the microorganism. The minimum bactericidalconcentration of the antimicrobial agent may be determined to be theconcentration of antimicrobial agent that exhibits an increase inmetabolic activity of the microorganism.

Depending on the type of microorganism, antimicrobial agents of interestmay include but are not limited to antibacterials, antifungals,antivirals, antiparasitics as well as antimicrobial pesticides. Suitableantibiotics include, but are not limited to, fluoroquinolones such asciprofloxacin, norfloxacin, ofloxacin, enoxacin, perfloxacin,fleroxacin, enrofloxacin, marbofloxacin, sarafloxacin, orbifloxacin,danofloxacin; aminoglycosides such as streptomycin, netilmicin,kanamycin, neomycin, tobramycin, amikacin, sisomicin, ribostamycin,dibekacin, framycetin, gentamycin, penicillins and aminopenicillins suchas penicillin, ampicillin, amoxicillin, nafcillin, oxacillin andticarcillin, cephalosporins such as ceftriaxone, cephalexin, cefadroxiland ceftiofur, β-lactams such as clavulanic acid which may be used inconjunction with penicillins or aminopenicillins, macrolides such asclarythromycin and erythromycin and other antibiotics such asdactinomycin, clindamycin, naladixic acid, chloramphenicol, rifamopin,clofazimine, spectinomycin, polymyxin B, colistin, minocycline,vancomycin, hygromycin B or C, fusidic acid, trimethoprim and cefotaxim.The concentration of antimicrobial agent in each sample vial may vary,depending on the type of antimicrobial agent, ranging from 0.001 μg/mLto 1000 μg/mL, such as 0.005 μg/mL to 900 μg/mL, such as from 0.01 μg/mLto 800 μg/mL, such as from 0.05 μg/mL to 700 μg/mL, such as from 0.1μg/mL to 500 μg/mL, such as from 0.5 μg/mL to 250 μg/mL and includingfrom 1 μg/mL to 100 μg/mL. In some embodiments, the amount ofantimicrobial agent ranges across the samples, such as from aconcentration that is below the minimum inhibitory concentration of theantimicrobial agent to a concentration that is greater than the minimumbactericidal concentration of the antimicrobial agent. For instance, theamount of antimicrobial agent may include increasing amounts in thesample vials being tested. For example, the sample vials may includeantimicrobial agents with concentrations that range from 0.125 μg/mL to8 μg/mL, such as concentrations of 0.125 μg/mL, 0.25 μg/mL, 0.5 μg/mL, 1μg/mL, 2 μg/mL, 4 μg/mL and 8 μg/mL.

In methods for characterizing the susceptibility of a microorganism toan antimicrobial agent according to the present disclosure, the amountof microorganism in each sample may be the same and may be 10 colonyforming unit (CFU) or more, such as 11 CFU or more, such as 12 CFU ormore, such as 13 CFU or more, such as 14 CFU or more, such as 15 CFU ormore, such as 20 CFU or more, such as 25 CFU or more and including 50CFU or more. In certain embodiments, methods include preparing amicroorganism-containing composition having a determined amount ofmicroorganism (e.g., 100 CFU) and aliquoting an equivalent volume of themicroorganism-containing composition into each of the samples.

The microorganism and antimicrobial agent is, in certain embodiments,incubated in the sample for a predetermined period of time beforeirradiating the sample the monochromatic light source, such as from 0.5minutes or more, such as for 1 minute or more, such as for 2 minutes ormore, such as for 5 minutes or more, such as for 10 minutes or more,such as for 15 minutes or more, such as for 20 minutes or more, such asfrom 30 minutes or more, such as for 45 minutes or more and includingfor 60 minutes or more. For example, the antimicrobial agent and themicroorganism may be incubated in the sample before being irradiated bythe monochromatic light source for a predetermined period of time thatranges from 0.5 minutes to 60 minutes, such as from 1 minute to 55minutes, such as from 2 minutes to 50 minutes, such as from 3 minutes to45 minutes, such as from 4 minutes to 40 minutes, such as from 5 minutesto 35 minutes and including from 10 minutes to 30 minutes, for examplefor 20 minutes.

Methods for Characterizing the Susceptibility of a Microorganism to anAntimicrobial Agent by Fluorescence Spectroscopy

Aspects of the present disclosure also include methods for determiningthe susceptibility of a microorganism to an antimicrobial agent byfluorescence spectroscopy. In some embodiments, methods includedetermining the minimum inhibitory concentration (MIC) of theantimicrobial agent (i.e., the lowest concentration of antimicrobialagent that inhibits growth of the microorganism). In other embodiments,methods include determining the minimum bactericidal concentration (MBC)of the antimicrobial agent (i.e., the lowest concentration ofantimicrobial agent required to kill the microorganism)

In embodiments, methods include irradiating a plurality of samples witha monochromatic light source, each sample having a microorganism and anantimicrobial agent, for a period of time and detecting fluorescencefrom each of the irradiated samples over the period of time, where eachsample has the same concentration of microorganism and differentconcentrations of antimicrobial agent; calculating a rate of change ofthe fluorescence in each sample by comparing a normalized rate of changein the intensity of the detected fluorescence produced by each samplewith a normalized rate of change of fluorescence produced by a control;and determining the susceptibility of the microorganism to theantimicrobial agent based on the calculated rate of change of thefluorescence of the plurality of samples. In some embodiments, eachsample is irradiated over a plurality of intensities by themonochromatic light source.

In some embodiments, methods further include comparing the calculatedrate of change of fluorescence for each sample. In some instances, thecomparing includes plotting the calculated rate of change offluorescence for each sample as a function of the log of theconcentration of antimicrobial agent in each sample. In otherembodiments, methods further include determining the concentration ofantimicrobial agent that exhibits a decrease or an increase in the rateof change of fluorescence. In still other embodiments, methods furtherinclude determining metabolic activity of the microorganism in eachsample based on the calculated rate of change of fluorescence for eachsample. For example, methods include determining the concentration ofantimicrobial agent that exhibits an increase or decrease in metabolicactivity.

The fluorescence produced by the sample and the control is detected from2500 cm⁻¹ to 3500 cm⁻¹, such as at 3000 cm⁻¹. In embodiments, thecontrol and sample include a reagent composition that includes ahydrophobic compound non-covalently associated with an albumin protein.The control sample is, in some instances, a composition that includesthe reagent composition and does not include a microorganism. Forexample, the control is a composition that has the same components asthe sample in the absence of microorganism. In some embodiments, thecontrol includes only the components of the reagent composition. Inother embodiments, the control includes the components of the reagentcomposition and microorganism-free plasma.

Methods for Determining the Phenotype of an Unknown Microorganism withResonant Raman Scattering

Aspects of the present disclosure also include methods for determiningthe phenotype of an unknown microorganism with Resonant Ramanscattering. In some embodiments, methods include determining whether anunknown microorganism produces a reactive metabolite (e.g., a freeradical-containing metabolite). In certain embodiments, the metaboliteis a reactive species capable of reacting with or cleaving a crosslink.

In embodiments, methods include irradiating with a monochromatic lightsource a sample comprising a microorganism, a crosslinking agent and analbumin protein over a plurality of intensities by the monochromaticlight source for a period of time and determining a rate of change inthe intensity of Resonant Raman scattering; calculating a net signal forthe sample by comparing a normalized rate of change in the intensity ofResonant Raman scattering for the sample with a normalized rate ofchange in the irradiation intensity of the sample by the monochromaticlight source; and determining crosslink cleavage based on the net signalof the sample, wherein the extent of crosslink cleavage is indicative ofthe phenotype of the microorganism. In certain embodiments, an increaseover time in the net signal of the sample is indicative that themicroorganism produces a metabolite that cleaves one or more crosslinksin the albumin protein.

Any suitable reactive crosslinking agent may be employed depending onthe type of microorganism being tested for, e.g., where themicroorganisms of interest may in certain embodiments produce apeptidase enzyme (e.g., a peptidase that cleaves a glutamic acid peptidebond). In some embodiments, the crosslinking agent is a disulfidecrosslinker (e.g., a compound having disulfide linkages that exchangesdisulfide bonds with a protein). In certain instances, the crosslinkingagent is also a glutamic acid derivative, such as a glutamic acidderivative having one or more disulfide linkages. In certainembodiments, the crosslinking agent is a compound of Formula (I):

where:

and R₂ are independently selected from hydrogen, alkyl, substitutedalkyl, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl,heteroalkyl, substituted heteroalkyl, heterocycloalkyl, substitutedheterocycloalkyl, heteroaryl and substituted heteroaryl;

X₁ and X₂ are independently selected from N, O, or S; and

R₃ is a hydrogen, alkyl, substituted alkyl, amino, halogen, cyano,alcohol or alkoxy.

In some embodiments, R₁, and R₂ are heteroaryl, X₁ and X₂ are N and R₃is amino.

In certain embodiments, the crosslinking agent is a compound of Formula(DS-1)

The crosslinking agent may be present in the sample in an amount wherethe molar ratio of crosslinking agent to albumin protein is from 1:10 to10:1, such as from 1:9 to 9:1, such as from 1:8 to 8:1, such as from 1:7to 7:1, such as from 1:6 to 6:1, such as from 1:5 to 5:1, such as from1:4 to 4:1, such as from 1:3 to 3:1, and including from 1:2 to 2:1. Incertain embodiments, the molar ratio of crosslinking agent to albuminprotein in samples of the subject methods is about 1:2.Methods for Determining the Phenotype of an Unknown Microorganism withFluorescence Spectroscopy

Aspects of the present disclosure also include methods for determiningthe phenotype of an unknown microorganism with fluorescencespectroscopy. In some embodiments, methods include determining whetheran unknown microorganism produces a reactive metabolite (e.g., a freeradical-containing metabolite). In certain embodiments, the metaboliteis a reactive species capable of reacting with or cleaving a crosslink.

In embodiments, methods include irradiating with a monochromatic lightsource a sample comprising a microorganism, a crosslinking agent and analbumin protein for a period of time and detecting fluorescence from thesample over the period of time; calculating a rate of change of thefluorescence by comparing a normalized rate of change in the intensityof the detected fluorescence produced by the sample with a normalizedrate of change of fluorescence produced by a control; and determiningcrosslink cleavage based on the calculated rate of change offluorescence of the sample, wherein the extent of crosslink cleavage isindicative of the phenotype of the microorganism. In some embodiments,the sample is irradiated over a plurality of intensities by themonochromatic light source.

The fluorescence produced by the sample and the control is detected from2500 cm⁻¹ to 3500 cm⁻¹, such as at 3000 cm⁻¹. In embodiments, thecontrol and sample include a reagent composition that includes ahydrophobic compound non-covalently associated with an albumin protein.The control sample is, in some instances, a composition that includesthe reagent composition and does not include a microorganism. Forexample, the control is a composition that has the same components asthe sample in the absence of microorganism. In some embodiments, thecontrol includes only the components of the reagent composition. Inother embodiments, the control includes the components of the reagentcomposition and microorganism-free plasma.

Systems for Non-Linear Resonant Raman Spectroscopy

Aspects of the present disclosure also include systems for non-linearResonant Raman spectroscopy. Systems according to certain embodimentsinclude a monochromatic light source, a detector for detecting ResonantRaman scattering and a processor having memory operably coupled to theprocessor, the memory having instructions stored thereon, which whenexecuted by the processor, cause the processor to: irradiate a samplewith a monochromatic light source at a first irradiation intensity and asecond irradiation intensity; determine the intensity of Resonant Ramanscattering at the first irradiation intensity and the second irradiationintensity; calculate a rate of change of the intensity of Resonant Ramanscattering in response to the change in irradiation intensity from thefirst irradiation intensity to the second irradiation intensity; andcompare the rate of change in the intensity of Resonant Raman scatteringwith the rate of change in the irradiation intensity by themonochromatic light source to determine the Resonant Raman response ofthe sample. Systems of interest also include (a) a monochromatic lightsource; (b) an optical adjustment component; (c) a photodetector; and(d) a processor comprising memory operably coupled to the processorwherein the memory comprises instructions stored thereon, which whenexecuted by the processor, cause the processor to: irradiate a sample ina sample holder with the monochromatic light source at a firstirradiation intensity and a second irradiation intensity for presetdurations; measure scattered light from the sample with thephotodetector; determine the intensity of Resonant Raman scattering andfluorescence scattering at the first irradiation intensity and thesecond irradiation intensity; calculate a rate of change in theintensity of Resonant Raman scattering and the intensity of fluorescencescattering; and correct the rate of change of the intensity of ResonantRaman scattering and the intensity of fluorescence scattering to obtaina net signal.

As summarized above, systems include one or more monochromatic lightsources. In embodiments, monochromatic light sources of interest outputlight having a narrow range of wavelengths, such as a range of 25 nm orless, such as 20 nm or less, such as 15 nm or less, such as 10 nm orless, such as 5 nm or less and including 2 nm or less. In certainembodiments, the monochromatic light source outputs a single wavelengthof light. In some instances, the monochromatic light source is a singlewavelength laser. In other instances, the monochromatic light source isa single wavelength LED.

In certain embodiments, the light source is a broadband light source inoptical communication with an optical adjustment component that narrowsthe irradiation bandwidth to a single wavelength. For example,monochromatic light irradiation of the sample for Resonant Ramanspectroscopy according to the subject methods may be achieved using abroadband light source such as a broadband halogen lamp, deuterium arclamp, xenon arc lamp, stabilized fiber-coupled broadband light source, abroadband LED with continuous spectrum, superluminescent emitting diode,semiconductor light emitting diode, wide spectrum LED white light sourceor a multi-LED integrated white light source coupled to one or moreoptical bandpass filters, diffraction gratings, monochromators or anycombination thereof.

In certain embodiments, systems include a laser. In some instances, thelaser is a continuous wave laser. In other instances, the laser is apulsed laser. In certain instances, the laser is a diode laser, such asan ultraviolet diode laser, a visible diode laser and a near-infrareddiode laser. In some instances, the monochromatic light source is adiode laser that outputs light at a wavelength from 375 nm to 1000 nm,such as from 405 nm to 875 nm, such as from 450 nm to 800 nm, such asfrom 500 nm to 650 nm and including from 525 nm to 625 nm. In otherinstances, the laser is a pulsed laser, such as a solid state laser. Incertain instances, the monochromatic light source is a solid-state laserthat outputs light at a wavelength from 375 nm to 1000 nm, such as from405 nm to 875 nm, such as from 450 nm to 800 nm, such as from 500 nm to650 nm and including from 525 nm to 625 nm. Other suitable lasers mayinclude, but are not limited to, helium-neon (HeNe) lasers, argonlasers, krypton lasers, xenon ion lasers, nitrogen lasers, carbondioxide lasers, carbon monoxide lasers, excimer lasers, hydrogenfluoride lasers, deuterium fluoride lasers, oxygen-iodine lasers,gas-phase iodine lasers, helium cadium lasers, helium mercury lasers,helium silver lasers, strontium vapor lasers, neon copper lasers, coppervapor laser, gold vapor laser, manganese vapor lasers, ruby lasers,Nd:YAG lasers, NdCrYAG lasers, Er:YAG lasers, Nd:YLF lasers, Nd:YVO₄lasers, Nd:YCa₄O(BO₃)₃ lasers, Nd:glass lasers, titanium sapphirelasers, thulium YAG lasers, ytterbium YAG lasers, Yb₂O₃ lasers,ytterbium doped glass lasers, holmium YAG lasers, chromium ZnSe lasers,cerium doped lithium strontium aluminum fluoride lasers, promethium 147doped phosphate glass lasers, chromium doped chrysoberyl lasers, erbiumdoped and erbium-ytterbium codoped glass lasers, trivalent uranium dopedcalcium fluoride lasers, samarium doped calcium fluoride lasers, GaNlasers, InGaN lasers, AlGaInP lasers, AlGaAs lasers, InGaAsP lasers,among other laser types. In certain embodiments, the monochromatic lightsource is a frequency doubled neodymium-doped yttrium aluminium garnetthat outputs light at 532 nm.

In some embodiments, systems include an optical adjustment componentthat is optically coupled to the laser. By “optical adjustment” is meantthat the laser light is change as desired before being conveyed to thesample. For example, systems may include one or more lenses,collimators, pinholes, mirrors, beam choppers, slits, gratings, filters,light refractors, and any combinations thereof. In certain embodiments,the optical adjustment component is a wavelength separator. The term“wavelength separator” is used herein in its conventional sense to referto an optical protocol for separating polychromatic light into itscomponent wavelengths. Wavelength separation, according to certainembodiments, may include selectively passing or blocking specificwavelengths or wavelength ranges of the polychromatic light. Wavelengthseparation protocols of interest which may be a part of or combined withthe subject connector, include but are not limited to, colored glass,bandpass filters, interference filters, dichroic mirrors, diffractiongratings, monochromators and combinations thereof, among otherwavelength separating protocols.

In some instances, the monochromatic light source for irradiating thesample is coupled to a collimator. The term “collimate” is used in itsconventional sense to refer to the optically adjusting the collinearityof light propagation or reducing divergence by the light of from acommon axis of propagation. In some instances, collimators areconfigured to narrow the spatial cross section of a light beam from themonochromatic light source. In other instances, the optical adjustmentcomponent is configured to change the direction of the light beam fromthe monochromatic light source, such as changing the propagation of thelight beam from the monochromatic light source by 1° or more, such as by5° or more, such as by 10° or more, such as by 15° or more, such as by20° or more, such as by 25° or more, such as by 30° or more, such as by45° or more, such as by 60° or more, such as by 75° or more andincluding changing the direction of light propagation by 90° or more. Inyet other instances, optical adjustment is a de-magnification protocolso as to decrease the dimensions of the light (e.g., beam spot), such asdecreasing the dimensions by 5% or more, such as by 10% or more, such asby 25% or more, such as by 50% or more and including decreasing thedimensions by 75% or more.

In certain embodiments, systems are configured for irradiating thesample at an interface (e.g., by focusing the monochromatic light sourcewith a collimator as described above) between the sample and a wall ofthe sample container. By “interface” is meant the space where thesurface of the container wall comes into contact with the sample in thecontainer. In embodiments, the subject systems may be configured suchthat the monochromatic light source irradiates the interface at a pointfrom about 0.01 mm to 2 mm from the surface of the container wall (i.e.,where the sample comes into contact with the container), such as from0.02 mm to 1.9 mm, such as from 0.03 mm to 1.8 mm, such as from 0.04 mmto 1.7 mm, such as from 0.05 mm to 1.6 mm, such as from 0.06 mm to 1.5mm, such as from 0.07 mm to 1.4 mm, such as from 0.08 mm to 1.3 mm, suchas from 0.09 mm to 1.2 mm, such as from 0.1 mm to 1 mm, for example 0.2mm from the surface of the container wall. In these embodiments, thesubject systems are configured to maintain the sample container (e.g.,glass vial as described below) substantially at rest (e.g., novibration, agitation, etc.) so that the velocity of the interfacialliquid layer irradiated by the monochromatic light source is near or atzero. For example, the liquid velocity of the interfacial sample layerirradiated by the monochromatic light source may be 10⁻² cm³/second orless, such as 10⁻³ cm³/second or less, such as 10⁻⁴ cm³/second or less,such as 10⁻⁵ cm³/second, such as 10⁻⁶ cm³/second, such as 10⁻⁷cm³/second or less, such as 10⁻⁸ cm³/second or less, such as 10⁻⁹cm³/second or less and including 10⁻¹⁰ cm³/second or less. In certainembodiments, the subject systems are configured such that the velocityof the sample at the interfacial layer when irradiated by themonochromatic light source in the subject methods is 0 cm³/second.

As described above, methods include irradiating a sample with themonochromatic light and determining the intensity of Resonant Ramanscattering and fluorescence. Systems for practicing the subject methodsinclude one or more detectors for detecting fluorescence and ResonantRaman scattering. Any convenient light detection protocol may beemployed, including but not limited to photosensors or photodetectorssuch as active-pixel sensors (APSs), quadrant photodiodes, wedgedetectors image sensors, charge-coupled devices (CCDs), intensifiedcharge-coupled devices (ICCDs), light emitting diodes, photon counters,bolometers, pyroelectric detectors, photoresistors, photovoltaic cells,photodiodes, photomultiplier tubes, phototransistors, quantum dotphotoconductors or photodiodes and combinations thereof, among otherphotodetectors. In certain embodiments, systems include one or moreCCDs.

Where the subject systems include more than one photodetector, eachphotodetector may be the same or a combination of different types ofphotodetectors. For example, where the subject systems include twophotodetectors, in some embodiments the first photodetector is aCCD-type device and the second photodetector is a CMOS-type device. Inother embodiments, both the first and second photodetectors are CCD-typedevices. In yet other embodiments, both the first and secondphotodetctors are CMOS-type devices. In yet other embodiments, the firstphotodetector is a CCD-type photodetector or CMOS-type device and thesecond photodetector is a photomultiplier tube. In still otherembodiments, the first photodetector and the second photodetector arephotomultiplier tubes.

The detector may be optically coupled to one or more optical adjustmentcomponents. For example, systems may include one or more lenses,collimators, pinholes, mirrors, beam choppers, slits, gratings, filters,light refractors, and any combinations thereof. In some embodiments, thedetector is coupled to a wavelength separator, such as colored glass,bandpass filters, interference filters, dichroic mirrors, diffractiongratings, monochromators and combinations thereof. In certainembodiments, Resonant Raman scattering from the sample is collected withfiber optics (e.g., fiber optics relay bundle) and the Resonant Ramanscattering is conveyed to the detector surface through the fiber optics.Any fiber optics light relay system may be employed to propagate thescattered light onto the active surface of the detector.

In certain embodiments, light detection systems include a collimatorpositioned adjacent to the sample container. The collimator may be anyconvenient collimating device, such as one or more mirrors or curvedlenses or a combination thereof. For example, the collimator is incertain instances a single collimating lens. In other instances, thecollimator is a collimating mirror. In yet other instances, thecollimator includes two lenses. In still other instances, the collimatorincludes a mirror and a lens. Where the collimator includes one or morelenses, the focal length of each collimating lens may vary, ranging from5 mm to 500 mm, such as from 6 mm to 475 mm, such as from 7 mm to 450mm, such as from 8 mm to 425 mm, such as from 9 mm to 400 mm, such asfrom 10 mm to 375 mm, such as from 12.5 mm to 350 mm and including afocal length ranging from 15 mm to 300 mm. In certain embodiments, thefocal length ranges from 400 mm to 500 mm, such as from 405 mm to 475mm, such as from 410 mm to 450 mm and including from 410 mm to 425 mm,such as 410 mm or 420 mm.

In embodiments, spectroscopy (e.g., non-linear Resonant Raman,fluorescence, etc.) is conducted at a substantially constanttemperature. As such, the subject systems are configured to maintain asubstantially constant temperature, such as where the temperature of thesystem changes by 5° C. or less, such as by 4.5° C. or less, such as by4° C. or less, such as by 3.5° C. or less, such as by 3° C. or less,such as by 2.5° C. or less, such as by 2° C. or less, such as by 1.5° C.or less, such as 1° C. or less, such as by 0.5° C. or less, such as by0.1° C. or less, such as by 0.05° C. or less, such as by 0.01° C. orless, such as by 0.005° C., such as by 0.001° C., such as by 0.0001° C.,such as by 0.00001° C. or less and including by 0.000001° C. or less. Inembodiments, the temperature of the system may be controlled by atemperature control subsystem which measures the system temperature andif necessary, controls the ambient conditions to maintain a desiredsystem temperature. Temperature subsystems may include any convenienttemperature control protocol, including, but not limited to heat sinks,fans, exhaust pumps, vents, refrigeration, coolants, heat exchanges,Peltier or resistive heating elements, among other types of temperaturecontrol protocols. As described in greater detail below, in someembodiments, systems include a processor having memory with instructionsthat include algorithm that measures the spectral drift of the laser atpredetermined times and calculates the thermal drift of the laser inresponse to the changes in temperature. Systems according to theseembodiments, also include algorithm for calculating a correction factorfor Resonant Raman spectroscopy for the measured thermal drift of thelaser.

Systems of interest may also include a sample holder for irradiating thesample with the monochromatic light source. The sample holder may be anysuitable shaped substrate or container for irradiating a sample anddetecting one or more of Resonant Raman scattering and fluorescencescattering. In some embodiments, the sample holder is a planar substrate(e.g., microscope slide). In other embodiments, the sample holder is amicrofluidic device having one or more microfluidic channels. In yetother embodiments, the sample holder is a container having across-sectional shape, where cross-sectional shapes of interest include,but are not limited to: rectilinear cross sectional shapes, e.g.,squares, rectangles, trapezoids, triangles, hexagons, etc., curvilinearcross-sectional shapes, e.g., circles, ovals, etc., as well as irregularshapes, e.g., a parabolic bottom portion coupled to a planar topportion, etc. The size of the sample holder may vary, depending on thevolume of the samples being irradiated, where holders of interest have alength that ranges from 5 mm to 100 mm, such as from 10 mm to 90 mm,such as from 15 mm to 85 mm, such as from 20 mm to 80 mm, such as from25 mm to 75 mm, such as from 30 mm to 70 mm and including from 35 mm to65 mm and a width (or cross-section where the container is cylindrical)of from 5 mm to 100 mm, such as from 10 mm to 90 mm, such as from 15 mmto 85 mm, such as from 20 mm to 80 mm, such as from 25 mm to 75 mm, suchas from 30 mm to 70 mm and including from 35 mm to 65 mm. Inembodiments, the sample holder may have a volume of from 0.1 cm³ to 10cm³, such as from 0.5 cm³ to 9 cm³, such as from 1 cm³ to 8 cm³, such asfrom 1.5 cm³ to 7 cm³, such as from 2 cm³ to 6 cm³, such as from 2.5 cm³to 5 cm³ including from 3 cm³ to 4 cm³.

The sample holder may be formed from any transparent material whichpasses the desired range of wavelength, including but not limited tooptical glass, borosilicate glass, Pyrex glass, ultraviolet quartz,infrared quartz, sapphire. In certain embodiments, the sample containeris glass having walls with a zwitterionic coating, such as azwitterionic silane coating (e.g., as described in the ExperimentalSection below). The sample container may also be formed from plastic,such as polycarbonates, polyvinyl chloride (PVC), polyurethanes,polyethers, polyamides, polyimides, or copolymers of thesethermoplastics, such as PETG (glycol-modified polyethyleneterephthalate), among other polymeric plastic materials, includingpolyester, where polyesters of interest may include, but are not limitedto poly(alkylene terephthalates) such as poly(ethylene terephthalate)(PET), bottle-grade PET (a copolymer made based on monoethylene glycol,terephthalic acid, and other comonomers such as isophthalic acid,cyclohexene dimethanol, etc.), poly(butylene terephthalate) (PBT), andpoly(hexamethylene terephthalate); poly(alkylene adipates) such aspoly(ethylene adipate), poly(1,4-butylene adipate), andpoly(hexamethylene adipate); poly(alkylene suberates) such aspoly(ethylene suberate); poly(alkylene sebacates) such as poly(ethylenesebacate); poly(ε-caprolactone) and poly(β-propiolactone); poly(alkyleneisophthalates) such as poly(ethylene isophthalate); poly(alkylene2,6-naphthalene-dicarboxylates) such as poly(ethylene2,6-naphthalene-dicarboxylate); poly(alkylene sulfonyl-4,4′-dibenzoates)such as poly(ethylene sulfonyl-4,4′-dibenzoate); poly(p-phenylenealkylene dicarboxylates) such as poly(p-phenylene ethylenedicarboxylates); poly(trans-1,4-cyclohexanediylalkylene dicarboxylates)such as poly(trans-1,4-cyclohexanediyl ethylene dicarboxylate);poly(1,4-cyclohexane-dimethylene alkylene dicarboxylates) such aspoly(1,4-cyclohexane-dimethylene ethylene dicarboxylate);poly([2.2.2]-bicyclooctane-1,4-dimethylene alkylene dicarboxylates) suchas poly([2.2.2]-bicyclooctane-1,4-dimethylene ethylene dicarboxylate);lactic acid polymers and copolymers such as (S)-polylactide,(R,S)-polylactide, poly(tetramethylglycolide), andpoly(lactide-co-glycolide); and polycarbonates of bisphenol A,3,3′-dimethylbisphenol A, 3,3′,5,5′-tetrachlorobisphenol A,3,3′,5,5′-tetramethylbisphenol A; polyamides such as poly(p-phenyleneterephthalamide); polyesters, e.g., polyethylene terephthalates, e.g.,Mylar™ polyethylene terephthalate; etc.

In embodiments, the sample holder may pass light that ranges from 100 nmto 1500 nm, such as from 150 nm to 1400 nm, such as from 200 nm to 1300nm, such as from 250 nm to 1200 nm, such as from 300 nm to 1100 nm, suchas from 350 nm to 1000 nm, such as from 400 nm to 900 nm and includingfrom 500 nm to 800 nm, for example 532 nm. As summarized above, systemsinclude one or more processors having memory that includes instructionsstored for practicing the methods described above. In some embodiments,the memory includes instructions stored thereon, which when executed bythe processor, cause the processor to: irradiate a sample with amonochromatic light source at a first irradiation intensity and a secondirradiation intensity; determine the intensity of Resonant Ramanscattering at the first irradiation intensity and the second irradiationintensity; calculate a rate of change of the intensity of Resonant Ramanscattering in response to the change in irradiation intensity from thefirst irradiation intensity to the second irradiation intensity; andcompare the rate of change in the intensity of Resonant Raman scatteringwith the rate of change in the irradiation intensity by themonochromatic light source to determine the Resonant Raman response ofthe sample.

In other embodiments, the memory includes instructions, which whenexecuted by the processor, cause the processor to irradiate the sampleover a plurality of intensities by the monochromatic light source over aperiod of time and determine a rate of change in the intensity ofResonant Raman scattering. In certain instances, the memory includesinstructions which when executed by the processor, cause the processorto: irradiate a first sample over a plurality of intensities by themonochromatic light source for a period of time and determine a rate ofchange in the intensity of Resonant Raman scattering for the firstsample; calculate a net signal of the first sample by comparing anormalized rate of change in the intensity of Resonant Raman scatteringfor the first sample with a normalized rate of change in the irradiationintensity of the first sample by the monochromatic light source;irradiate a second sample over a plurality of intensities by themonochromatic light source for the period of time and determine a rateof change in the intensity of Resonant Raman scattering for the secondsample; and calculate a net signal of the second sample by comparing anormalized rate of change in the intensity of Resonant Raman scatteringfor the second sample with a normalized rate of change in theirradiation intensity of the second sample by the monochromatic lightsource. The memory may also include instructions, in certainembodiments, which when executed by the processor, cause the processorto determine that the first sample comprises a different gaseouscomposition from the second sample based on the compared net signals. Inother embodiments, the memory includes instructions which when executedby the processor, cause the processor to determine that the first sampleor the second sample comprises actively metabolizing microorganismsbased on the compared net signals.

Aspects also include systems for determining the presence of absence ofa microorganism in a sample. Systems according to certain embodiments,include a processor comprising memory operably coupled to the processorwherein the memory includes instructions stored thereon, which whenexecuted by the processor, cause the processor to: irradiate a sampleover a plurality of intensities by a monochromatic light source for aperiod of time and calculating a rate of change in the intensity ofResonant Raman scattering for the first sample; calculate a net signalof the sample by comparing a normalized rate of change in the intensityof Resonant Raman scattering for the sample with a normalized rate ofchange in the irradiation intensity of the sample by the monochromaticlight source; and determine the presence or absence of a microorganismin the sample based on the net signal of the sample. In some instances,the memory further includes instructions, which when executed by theprocessor, cause the processor to determine that a microorganism ispresent when the net signal of the sample is above a predeterminedthreshold. The threshold may vary, ranging from −0.5 to −4×10⁻⁵/sec,such as from −0.5 to −1×10⁻⁵/sec, such as from −1 to −2×10⁻⁵/sec andincluding a predetermined threshold where the net signal is −1×10⁻⁵/sec.In some embodiments, the one or more present thresholds are set byimplementing the method above on one or more control samples thatcontains an inoculum in an amount at a lower limit of concentration in aclinically infected sample. In some embodiments, the memory includesinstructions which when executed by the processor, cause the processorto determine that a microorganism is present when the net signal of thesample exceeds the threshold by 1% or more of the threshold value, suchas 5% or more, such as 10% or more, such as 15% or more, such as 25% ormore, such as 50% or more, such as 75% or more and including 90% ormore, for example, by 2-fold or more, such as 3-fold or more, such as5-fold or more and including 10-fold or more.

In certain embodiments, systems include a processor comprising memoryoperably coupled to the processor wherein the memory includesinstructions stored thereon, which when executed by the processor, causethe processor to determine the presence of a microorganism by comparingthe net signal of two different samples. In some embodiments, one of thesamples is a reference sample that does not contain a microorganism. Inthese embodiments, the memory may include instructions which whenexecuted by the processor, cause the processor to: irradiate a firstsample over a plurality of intensities by a monochromatic light sourcefor a period of time and calculate a rate of change in the intensity ofResonant Raman scattering for the first sample; calculate a net signalof the first sample by comparing a normalized rate of change in theintensity of Resonant Raman scattering for the first sample with anormalized rate of change in the irradiation intensity of the firstsample by the monochromatic light source; irradiate a second sample overa plurality of intensities by the monochromatic light source for theperiod of time and determining a rate of change in the intensity ofResonant Raman scattering for the second sample; calculate a net signalof the second sample by comparing a normalized rate of change in theintensity of Resonant Raman scattering for the second sample with anormalized rate of change in the irradiation intensity of the secondsample by the monochromatic light source; and determine the presence orabsence of a microorganism in one or more of the first sample or thesecond sample by comparing the net signal of the first sample with thenet signal of the second sample. In some instances, the memory includesinstructions, which when executed by the processor, cause the processorto determine that a microorganism is present in the second sample whenthe net signal of the second sample is greater than the net signal ofthe first sample. In other instances, the memory includes instructions,which when executed by the processor, cause the processor to determinethat a microorganism is present in the first sample when the net signalof the first sample is greater than the net signal of the second sample.Where the first sample is a reference sample, the memory includesinstructions, which when executed by the processor, cause the processorto determine that a microorganism is present in the second sample whenthe net signal of the second sample is greater than the net signal ofthe reference sample.

Aspects also include systems for calculating signal-to-noise ratio innon-linear Resonant Raman spectroscopy. Systems according to certainembodiments, include a processor comprising memory operably coupled tothe processor wherein the memory includes instructions stored thereon,which when executed by the processor, cause the processor to: irradiatea first sample over a plurality of intensities by a monochromatic lightsource for a period of time and determining a rate of change in theintensity of Resonant Raman scattering for the first sample; calculatean average rate of change in the intensity of Resonant Raman scatteringby the first sample to give a first average rate of change; calculate astandard deviation for the first average rate of change; irradiate asecond sample over a range of intensities by the monochromatic lightsource for the period of time and determine a rate of change in theintensity of Resonant Raman scattering for the second sample; calculatean average rate of change in the intensity of Resonant Raman scatteringby the second sample to give a second average rate of change; calculatea standard deviation for the second average rate of change; subtract thesecond average rate of change from the first average rate of change togive a signal average rate of change; add the first standard deviationand the second standard deviation to give a signal standard deviation;and divide the signal average rate of change by the signal standarddeviation to determine a signal-to-noise ratio for Resonant Ramanresponse.

Aspects of the present disclosure also include subsystems for correctingfor thermal drift in the monochromatic light source in non-linearResonant Raman spectroscopy. Where the subject systems include a laser,subsystems of interest are configured to correct for thermal drift in alaser. Systems according to certain embodiments, include a processorcomprising memory operably coupled to the processor wherein the memoryincludes instructions stored thereon, which when executed by theprocessor, cause the processor to: irradiate a reference compositionover a plurality of intensities by the monochromatic light source forthe period of time and determining a rate of change in the intensity ofResonant Raman scattering, wherein the reference composition comprises areference compound that exhibits no change in the intensity of ResonantRaman scattering in response to the change in irradiation intensity bythe monochromatic light source; and calculate a net signal of thereference composition by comparing the rate of change in the intensityof Resonant Raman scattering for the reference composition with the rateof change in the irradiation intensity of the reference composition bythe monochromatic light source to determine if the monochromatic lightsource exhibits thermal drift.

Where the system determines that the monochromatic light source (e.g.,laser) exhibits thermal drift, the system may be configured to correctfor the thermal drift in non-linear Resonant Raman spectroscopy. Inthese embodiments, the subject systems may include memory withinstructions, which when executed by the processor, cause the processorto: irradiate a sample over a range of intensities by a monochromaticlight source for a period of time and determining a rate of change inthe intensity of Resonant Raman scattering; multiply the net signal ofthe reference composition with the rate of change of irradiationintensity of the sample by the monochromatic light source to produce acorrection factor; and subtract the correction factor from thedetermined rate of change in the intensity of Resonant Raman scatteringfor the sample to correct for the thermal drift of the monochromaticlight source.

Aspects also include systems for characterizing the antimicrobialsusceptibility of a microorganism to an antimicrobial agent withResonant Raman scattering. Systems according to certain embodiments,include a processor comprising memory operably coupled to the processorwherein the memory includes instructions stored thereon, which whenexecuted by the processor, cause the processor to: irradiate a pluralityof samples, each sample comprising a microorganism and an antimicrobialagent over a plurality of intensities by the monochromatic light sourcefor a period of time and determining a rate of change in the intensityof Resonant Raman scattering for each irradiated sample, wherein eachsample comprises the same concentration of microorganism and differentconcentrations of antimicrobial agent; calculate a net signal for eachsample by comparing a normalized rate of change in the intensity ofResonant Raman scattering for each sample with a normalized rate ofchange in the irradiation intensity of each sample by the monochromaticlight source; and determine the susceptibility of the microorganism tothe antimicrobial agent based on the net signals the plurality ofsamples. In some embodiments, the memory includes instructions storedthereon, which when executed by the processor, cause the processor tocompare the net signal for each sample. In some instances, the memoryfurther includes instructions stored thereon, which when executed by theprocessor, cause the processor to plot the net signal for each sample asa function of the log of the concentration of antimicrobial agent ineach sample. In some instances, the memory includes instructions storedthereon, which when executed by the processor, cause the processor todetermine the concentration of antimicrobial agent that exhibits adecrease in the net signal. For example, the memory may includeinstructions stored thereon, which when executed by the processor, causethe processor to determine the concentration of antimicrobial agent thatexhibits an increase in the net signal.

In other embodiments, the memory includes instructions stored thereon,which when executed by the processor, cause the processor to determinemetabolic activity of the microorganism in each sample based on the netsignal for each sample. For instance, the memory may includeinstructions stored thereon, which when executed by the processor, causethe processor to determine the concentration of antimicrobial agent thatexhibits a decrease in metabolic activity or cause the processor todetermine the concentration of antimicrobial agent that exhibits anincrease in metabolic activity.

Aspects also include systems for characterizing the antimicrobialsusceptibility of a microorganism to an antimicrobial agent withfluorescence spectroscopy. Systems according to certain embodiments,include a processor comprising memory operably coupled to the processorwherein the memory includes instructions stored thereon, which whenexecuted by the processor, cause the processor to: irradiate a pluralityof samples comprising a microorganism, each sample comprising amicroorganism and an antimicrobial agent by the monochromatic lightsource for a period of time and detecting fluorescence from each of theirradiated samples over the period of time, wherein each samplecomprises the same concentration of microorganism and differentconcentrations of antimicrobial agent; calculate a rate of change of thefluorescence in each sample by comparing a normalized rate of change inthe intensity of the detected fluorescence produced by each sample witha normalized rate of change of fluorescence produced by a control; anddetermine the susceptibility of the microorganism to the antimicrobialagent based on the calculated rate of change of the fluorescence of theplurality of samples. In some embodiments, the system is configured toirradiate each sample over a plurality of intensities by themonochromatic light source. In some embodiments, the memory furtherincludes instructions, which when executed by the processor, cause theprocessor to compare the calculated rate of change of fluorescence foreach sample. In these instances, comparing may include plotting thecalculated rate of change of fluorescence for each sample as a functionof the log of the concentration of antimicrobial agent in each sample.In other embodiments, the memory further includes instructions, whichwhen executed by the processor, cause the processor to determine theconcentration of antimicrobial agent that exhibits a decrease orincrease in the rate of change of fluorescence. In still otherembodiments, the memory further includes instructions, which whenexecuted by the processor, cause the processor to determine theconcentration of antimicrobial agent that exhibits a decrease orincrease in metabolic activity.

Aspects also include systems for determining the phenotype of an unknownmicroorganism in a sample with Resonant Raman scattering. Systemsaccording to certain embodiments, include a processor comprising memoryoperably coupled to the processor wherein the memory includesinstructions stored thereon, which when executed by the processor, causethe processor to: irradiate with a monochromatic light source a samplecomprising a microorganism, a crosslinking agent and a protein over aplurality of intensities by the monochromatic light source for a periodof time and determining a rate of change in the intensity of ResonantRaman scattering; calculate a net signal for the sample by comparing anormalized rate of change in the intensity of Resonant Raman scatteringfor the sample with a normalized rate of change in the irradiationintensity of the sample by the monochromatic light source; and determinecrosslink cleavage based on the net signal of the sample, wherein theextent of crosslink cleavage is indicative of the phenotype of themicroorganism.

Aspects also include systems for determining the phenotype of an unknownmicroorganism in a sample with fluorescence spectroscopy. Systemsaccording to certain embodiments, include a processor comprising memoryoperably coupled to the processor wherein the memory includesinstructions stored thereon, which when executed by the processor, causethe processor to: irradiate with a monochromatic light source a samplecomprising a microorganism, a crosslinking agent and an albumin proteinfor a period of time and detect fluorescence from the sample over theperiod of time; calculate a rate of change of the fluorescence bycomparing a normalized rate of change in the intensity of the detectedfluorescence produced by the sample with a normalized rate of change offluorescence produced by a control; and determine crosslink cleavagebased on the calculated rate of change of fluorescence of the sample,wherein the extent of crosslink cleavage is indicative of the phenotypeof the microorganism. In some embodiments, the system is configured toirradiate the sample over a plurality of intensities by themonochromatic light source.

In some embodiments, the crosslinking agent is a disulfide crosslinker(e.g., a compound having disulfide linkages that exchanges disulfidebonds with a protein). In certain instances, the crosslinking agent isalso a glutamic acid derivative, such as a glutamic acid derivativehaving one or more disulfide linkages. In certain embodiments, thecrosslinking agent is a compound of Formula (I):

where:

R₁, and R₂ are independently selected from hydrogen, alkyl, substitutedalkyl, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl,heteroalkyl, substituted heteroalkyl, heterocycloalkyl, substitutedheterocycloalkyl, heteroaryl and substituted heteroaryl;

X₁ and X₂ are independently selected from N, O, or S; and

R₃ is a hydrogen, alkyl, substituted alkyl, amino, halogen, cyano,alcohol or alkoxy.

In some embodiments, R₁, and R₂ are heteroaryl, X₁ and X₂ are N and R₃is amino.

In certain embodiments, the crosslinking agent is a compound of Formula(DS-1)

The crosslinking agent may be present in the sample in an amount wherethe molar ratio of crosslinking agent to albumin protein is from 1:10 to10:1, such as from 1:9 to 9:1, such as from 1:8 to 8:1, such as from 1:7to 7:1, such as from 1:6 to 6:1, such as from 1:5 to 5:1, such as from1:4 to 4:1, such as from 1:3 to 3:1 t, and including from 1:2 to 2:1. Incertain embodiments, the molar ratio of crosslinking agent to albuminprotein in samples of the subject methods is about 1:2. As describedabove, the subject systems include a processor with memory operablycoupled to the processor having instructions for practicing the methodsdescribed herein. Systems may include non-transitory computer readablestorage mediums for storing the above-described instructions. Computerreadable storage mediums may be employed on one or more computers forcomplete automation or partial automation of a system for practicingmethods described herein. In certain embodiments, instructions inaccordance with the methods described herein can be coded onto acomputer-readable medium in the form of “programming”, where the term“computer readable medium” as used herein refers to any non-transitorystorage medium that participates in providing instructions and data to acomputer for execution and processing. Examples of suitablenon-transitory storage media include a floppy disk, hard disk, opticaldisk, magneto-optical disk, CD-ROM, CD-R, magnetic tape, non-volatilememory card, ROM, DVD-ROM, Blue-ray disk, solid state disk, and networkattached storage (NAS), whether or not such devices are internal orexternal to the computer. A file containing information can be “stored”on computer readable medium, where “storing” means recording informationsuch that it is accessible and retrievable at a later date by acomputer.

The computer-implemented method described herein can be executed usingprogramming that can be written in one or more of any number of computerprogramming languages. Such languages include, for example, Java (SunMicrosystems, Inc., Santa Clara, Calif.), Visual Basic (Microsoft Corp.,Redmond, Wash.), and C++ (AT&T Corp., Bedminster, N.J.), as well as anymany others.

The computer readable storage medium may be employed on one or morecomputer systems having a display and operator input device. Operatorinput devices may, for example, be a keyboard, mouse, or the like. Theprocessing module includes a processor which has access to a memoryhaving instructions stored thereon for performing the steps of thesubject methods. The processing module may include an operating system,a graphical user interface (GUI) controller, a system memory, memorystorage devices, and input-output controllers, cache memory, a databackup unit, and many other devices. The processor may be a commerciallyavailable processor or it may be one of other processors that are orwill become available. The processor executes the operating system andthe operating system interfaces with firmware and hardware in awell-known manner, and facilitates the processor in coordinating andexecuting the functions of various computer programs that may be writtenin a variety of programming languages, such as Java, Perl, C++, otherhigh level or low level languages, as well as combinations thereof, asis known in the art. The operating system, typically in cooperation withthe processor, coordinates and executes functions of the othercomponents of the computer. The operating system also providesscheduling, input-output control, file and data management, memorymanagement, and communication control and related services, all inaccordance with known techniques.

TECHNICAL FEATURES

Certain technical features of the subject methods are provided below.

Rate of Change of Resonant Raman Peaks

In Resonant Raman spectroscopy, the intensity of the observed Raman bandcan be described by Equation 1:

I _(R) =I _(o)(ν_(o)−ν_(mn))⁴Σ|(α_(ij))_(mn)|²  Equation 1

where I_(o) & ν_(o) are the Intensity and frequency of the laser, I_(R)is the intensity of the Raman band observed at frequency ν_(mn). And thepolarizability can be defined by the difference between the laserfrequency and the energy difference between the ground and excitedstates.)

(α_(ij))_(mn)∝(ν_(em)−ν₀)⁻¹.

Using these fundamental terms, it can be seen that the rate of change ofthe intensity of the Raman band scales with the rate of change of theintensity of the laser and the rate of change of the polarizability term

$\begin{matrix}{{\frac{1}{I_{R}}\frac{\delta\; I_{R}}{\delta\; t}} = {{\frac{1}{I_{o}}\frac{\delta\; I_{o}}{\delta\; t}} + \frac{\delta\;\ln\mspace{14mu}\Sigma{\left( \alpha_{ij} \right)_{mn}}^{2}}{\delta\; t}}} & {{Equation}\mspace{14mu} 2}\end{matrix}$

Absent changes in the polarizability terms (the 2^(nd) term in

${\frac{1}{I_{R}}\frac{\delta\; I_{R}}{\delta\; t}} = {{\frac{1}{I_{o}}\frac{\delta\; I_{o}}{\delta\; t}} + \frac{\delta\;\ln\mspace{14mu}\Sigma{\left( \alpha_{ij} \right)_{mn}}^{2}}{\delta\; t}}$

Equation 2 above), the normalized rate of change of Raman bands will beequal to the normalized rate of change laser intensity. If thepolarizability terms change with laser intensity (for instance, if theexcited state is being altered by changes in laser intensity), or if thepolarizability term is changing by itself (for instance, if the excitedstate is being changed by an ongoing chemical/physical reaction) thenthe two terms will not be equal. In this scenario, the rate of change ofRaman peak intensity can be used to characterize any changes that canaffect the polarizability terms.

Aspects, including embodiments, of the subject matter described hereinmay be beneficial alone or in combination, with one or more otheraspects or embodiments. As will be apparent to those of skill in the artupon reading this disclosure, each of the individually numbered aspectsmay be used or combined with any of the preceding or followingindividually numbered aspects. This is intended to provide support forall such combinations of aspects and is not limited to combinations ofaspects explicitly provided below:

1. A method of determining a Resonant Raman response of a sample, themethod comprising:

irradiating a sample with a monochromatic light source at a firstirradiation intensity and a second irradiation intensity;

determining the intensity of Resonant Raman scattering at the firstirradiation intensity and the second irradiation intensity;

calculating a rate of change of the intensity of Resonant Ramanscattering in response to the change in irradiation intensity from thefirst irradiation intensity to the second irradiation intensity; and

comparing the rate of change in the intensity of Resonant Ramanscattering with the rate of change in the irradiation intensity by themonochromatic light source to determine changes to the Resonant Ramanresponse of the sample.

2. The method according to 1, wherein the Resonant Raman response of thesample is indicative of a physical change over time in the sample.3. The method according to 1, wherein the Resonant Raman response of thesample is indicative of a chemical change over time in the sample.4. The method according to 1, wherein the Resonant Raman response of thesample is indicative of the presence of an actively metabolizingmicroorganism in the sample.5. The method according to any one of 1-4, wherein the monochromaticlight source is a laser.6. The method according to any one of 1-5, wherein the sample comprisesa hydrophobic compound and an albumin protein.7. The method according to 6, wherein the hydrophobic compound is acarotenoid.8. The method according to 7, wherein the hydrophobic compound islycopene.9. The method according to any one of 6-8, wherein the hydrophobiccompound is non-covalently associated with the albumin protein.10. The method according to any one of 1-9, wherein the sample comprisesa free radical scavenger.11. The method according to 10, wherein the free radical scavenger isnon-covalently associated with an albumin protein.12. The method according to any one of 10-11 wherein the free-radicalscavenger comprises bilirubin or a derivative thereof.13. The method according to 12, wherein bilirubin or a derivativethereof is present in the sample at a concentration of from 0.5 μM to 2μM.14. The method according to 12, wherein bilirubin or a derivativethereof is present in the sample at a concentration of from 0.25 μM to1.75 μM.15. The method according to any one of 1-9, wherein the sample comprisesa reducing agent.16. The method according to 15, wherein the reducing agent isglutathione or a derivative thereof.17. The method according to any one of 15-16, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.18. The method according to any one of 1-17, wherein the methodcomprises irradiating the sample over a plurality of irradiationintensities by the monochromatic light source over a period of time anddetermining a rate of change in the intensity of Resonant Ramanscattering.19. The method according to any one of 1-17, wherein the methodcomprises:

irradiating a first sample over a plurality of intensities by themonochromatic light source for a period of time and determining a rateof change in the intensity of Resonant Raman scattering for the firstsample;

calculating a net signal of the first sample by comparing a normalizedrate of change in the intensity of Resonant Raman scattering for thefirst sample with a normalized rate of change in the irradiationintensity of the first sample by the monochromatic light source;

irradiating a second sample over a plurality of intensities by themonochromatic light source for the period of time and determining a rateof change in the intensity of Resonant Raman scattering for the secondsample; and

calculating a net signal of the second sample by comparing a normalizedrate of change in the intensity of Resonant Raman scattering for thesecond sample with a normalized rate of change in the irradiationintensity of the second sample by the monochromatic light source.

20. The method according to 18, further comprising comparing thecalculated net signal of the first sample with the calculated net signalof the second sample.21. The method according to 20, further comprising determining that thefirst sample and the second sample are different based on the comparedcalculated net signals.22. The method according to 20, further comprising determining that thefirst sample comprises a different gaseous composition from the secondsample based on the compared calculated net signals.23. The method according to 20, further comprising determining that thefirst sample or the second sample comprises actively metabolizingmicroorganisms based on the compared calculated net signals.24. The method according to any one of 1-23, wherein the sample isirradiated in a sample container.25. The method according to 24, wherein the sample container is a glassvial.26. The method according to 25, wherein the glass vial comprises wallshaving a zwitterionic coating.27. The method according to 26, wherein the glass vial comprises wallshaving a zwitterionic silane coating.28. The method according to any one of 25-27, wherein the sample isirradiated at an interface between the sample and the container wall.29. The method according to 28, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.30. The method according to 29, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.31. The method according to 30, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.32. The method according to any one of 29-31, wherein the monochromaticlight source is focused with a collimating lens.33. The method according to any one of 1-32, wherein the sample furthercomprises a crosslinking agent.34. The method according to 33, wherein the crosslinking agent is adisulfide crosslinker.35. The method according to any one of 33-34, wherein the crosslinkingagent is a glutamic acid derivative.36. The method according to 35, wherein the crosslinking agent comprisesa compound of Formula (I):

37. The method according to any one of 33-36, wherein the crosslinkingagent is present in the sample in an amount such that the molar ratio ofcrosslinking agent to albumin protein is from 1:10 to 10:1.38. The method according to 37, wherein the crosslinking agent ispresent in the sample in an amount such that the molar ratio ofcrosslinking agent to albumin protein is about 1:2.

Methods for Detecting a Microorganism in a Sample

1. A method for determining the presence of a microorganism in a sample,the method comprising:

irradiating a sample over a plurality of intensities by a monochromaticlight source for a period of time and calculating a rate of change inthe intensity of Resonant Raman scattering for the sample;

calculating a net signal of the sample by comparing a normalized rate ofchange in the intensity of Resonant Raman scattering for the sample witha normalized rate of change in the irradiation intensity of the sampleby the monochromatic light source; and

determining the presence of a microorganism in the sample based on thecalculated net signal of the sample.

2. The method according to 1, wherein a microorganism is determined tobe present when the calculated net signal of the sample is above apredetermined threshold.3. The method according to 2, wherein the predetermined threshold is anet signal of 1.4. The method according to any one of 1-3, wherein the monochromaticlight source is a laser.5. The method according to any one of 1-4, wherein the sample comprisesa hydrophobic compound non-covalently associated with an albuminprotein.6. The method according to any one of 1-5, further comprising a freeradical scavenger.7. The method according to 6, wherein the free radical scavengercomprises bilirubin or a derivative thereof.8. The method according to 7, wherein the bilirubin or derivativethereof is present at a concentration of from 0.5 μM to 2 μM.9. The method according to 7, wherein the bilirubin is present at aconcentration of from 0.25 μM to 1.75 μM.10. The method according to any one of 1-9, wherein the sample comprisesa reducing agent.11. The method according to 10, wherein the reducing agent isglutathione or a derivative thereof.12. The method according to any one of 10-11, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.13. The method according to any one of 1-12, wherein the sample isirradiated in a sample container.14. The method according to 13, wherein the sample container is a glassvial.15. The method according to 14, wherein the glass vial comprises wallshaving a zwitterionic coating.16. The method according to 15, wherein the glass vial comprises wallshaving a zwitterionic silane coating.17. The method according to any one of 14-16, wherein the sample isirradiated at an interface between the sample and the container wall.18. The method according to 17, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.19. The method according to 18, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.20. The method according to 19, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.21. The method according to any one of 18-20, wherein the monochromaticlight source is focused with a collimating lens.22. A method for determining the presence of a microorganism in asample, the method comprising:

irradiating a first sample over a plurality of intensities by amonochromatic light source for a period of time and calculating a rateof change in the intensity of Resonant Raman scattering for the firstsample;

calculating a net signal of the first sample by comparing a normalizedrate of change in the intensity of Resonant Raman scattering for thefirst sample with a normalized rate of change in the irradiationintensity of the first sample by the monochromatic light source;

irradiating a second sample over a plurality of intensities by themonochromatic light source for the period of time and determining a rateof change in the intensity of Resonant Raman scattering for the secondsample;

calculating a net signal of the second sample by comparing a normalizedrate of change in the intensity of Resonant Raman scattering for thesecond sample with a normalized rate of change in the irradiationintensity of the second sample by the monochromatic light source; and

determining the presence of a microorganism in one or more of the firstsample or the second sample by comparing the net signal of the firstsample with the net signal of the second sample.

23. The method according to any one of 22, wherein a microorganism isdetermined to be present in the second sample when the calculated netsignal of the second sample is greater than the calculated net signal ofthe first sample.24. The method according to any one of 22, wherein a microorganism isdetermined to be present in the first sample when the calculated netsignal of the first sample is greater than the calculated net signal ofthe second sample.25. The method according to any one of 22-24, wherein the monochromaticlight source is a laser.26. The method according to any one of 22-25, wherein the samplecomprises a hydrophobic compound non-covalently associated with analbumin protein.27. The method according to 26, further comprising a free radicalscavenger.28. The method according to 27, wherein the free radical scavengercomprises bilirubin or a derivative thereof.29. The method according to 28, wherein the bilirubin or derivativethereof is present at a concentration of from 0.5 μM to 2 μM.30. The method according to 28, wherein the bilirubin is present at aconcentration of from 0.25 μM to 1.75 μM.31. The method according to any one of 22-30, wherein the samplecomprises a reducing agent.32. The method according to 31, wherein the reducing agent isglutathione or a derivative thereof.33. The method according to any one of 31-32, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.34. The method according to any one of 22-33, wherein the sample isirradiated in a sample container.35. The method according to 34, wherein the sample container is a glassvial.36. The method according to 35, wherein the glass vial comprises wallshaving a zwitterionic coating.37. The method according to 36, wherein the glass vial comprises wallshaving a zwitterionic silane coating.38. The method according to any one of 34-37, wherein the sample isirradiated at an interface between the sample and the container wall.39. The method according to claim 38, wherein the monochromatic lightsource is focused at a position at the interface between the sample andthe container wall.40. The method according to 39, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.41. The method according to 39, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.42. The method according to any one of 39-41, wherein the monochromaticlight source is focused with a collimating lens.

Methods for Determining the Presence of Microorganism in a Sample

1. A method for determining the presence of a microorganism in a sample,the method comprising:

(a) combining in a sample holder the sample with a reagent that containsalbumin with an incorporated ligand;

(b) irradiating the sample with a monochromatic light source that isabsorbed by the ligand, with either an invariant light intensity or onethat varies over time focused at an interface between the sample and asurface of the sample holder; and

(c) collecting scattered light from the irradiated sample and measuringa Raman signal and a fluorescence signal from the scattered light at aplurality of different times; and

(d) calculating a rate of change in intensity of the Raman signal andfluorescence signal for the sample over time; and

(e) correcting the calculated rates of change in the intensities of theRaman signal and the fluorescence signal to obtain a net signal; and

(f) determining the presence of a microorganism in the sample based on acomparison of the net signal versus one or more preset thresholds.

2. The method according to 1, wherein the one or more present thresholdsof 1f are set by implementing the method of claim 1 on one or morecontrol samples that contains an inoculum in an amount at a lower limitof concentration in a clinically infected sample.3. The method according to 1, wherein the ligand islycopene.4. The method according to 1, wherein the monochromatic light source isa laser.5. The method according to 4, wherein the laser irradiates the sample at532 nm.6. The method according to 1, wherein correcting the rate of change inthe intensities of the Raman signal and the fluorescence signalcomprises characterizing a spectral output from a standard sample.7. The method according to 6, wherein the standard is a NIST SRM 2242.8. The method according to claim 1, wherein correcting the rate ofchange in the intensities of the Raman signal comprises characterizing afluorescence output from the reagent.9. The method according to 1, further comprising pretreating the albuminof the reagent with a reducing agent prior to incorporating the ligand.10. The method according to 9, wherein pretreating the albumin with thereducing agent is sufficient to reduce disulfide bonds.11. The method according to 9, wherein the reducing agent is glutathioneor bilirubin.12. The method according to 10, further comprising contacting thepretreated albumin with a disulfide crosslinking agent.13. The method according to 12, where the disulfide crosslinking agentcomprises a core that is cleaved by enzymes or a metabolite produced bythe microorganism in the sample.14. The method according to 10, wherein the crosslinking agent comprisesa compound of Formula (I):

15. The method according to 1, wherein the sample holder is a glassvial.16. The method according to 15, wherein a surface of the glass vialcomprises a coating that modifies the absorption of albumin on the glasssurface.17. The method according to 16, wherein the coating is a zwitterioniccoating.18. The method according to 1, where the reagent comprises anantimicrobial composition.19. The method according to 18, further comprising plotting the netsignal against antimicrobial concentration,

wherein a minima in the plot is used to estimate minimum bactericidalconcentration of the antimicrobial composition; and

wherein a breakpoint in the plot is used to estimate minimum inhibitoryconcentration of the antimicrobial composition.

Methods for Correcting for Drifts in Laser Power During Non-Linear RamanSpectroscopy

1. A method comprising:

irradiating a reference composition over a plurality of intensities by amonochromatic light source for the period of time and determining a rateof change in the intensity of Resonant Raman scattering, wherein thereference composition comprises a reference compound that exhibits nochange in the intensity of Resonant Raman scattering in response to thechange in irradiation intensity by the monochromatic light source; and

calculating a net signal of the reference composition by comparing therate of change in the intensity of Resonant Raman scattering for thereference composition with the rate of change in the irradiationintensity of the reference composition by the monochromatic light sourceto determine if the monochromatic light source exhibits thermal drift.

2. The method according to 1, further comprising:

irradiating a sample over a range of intensities by a monochromaticlight source for a period of time and determining a rate of change inthe intensity of Resonant Raman scattering;

multiplying the net signal of the reference composition with the rate ofchange of irradiation intensity of the sample by the monochromatic lightsource to produce a correction factor; and

subtracting the correction factor from the determined rate of change inthe intensity of Resonant Raman scattering for the sample to correct forthe thermal drift of the monochromatic light source.

3. The method according to any one of 1-2, wherein the monochromaticlight source is a laser.4. The method according to 3, wherein the laser is a solid-state laserthat irradiates at 532 nm.5. The method according to any one of 1-4, wherein the sample comprisesa hydrophobic compound non-covalently associated with an albuminprotein.6. The method according to 5, further comprising a free radicalscavenger.7. The method according to 6, wherein the free radical scavengercomprises bilirubin or a derivative thereof.8. The method according to 7, wherein bilirubin or derivative thereof ispresent at a concentration of from 0.5 μM to 2 μM.9. The method according to 7, wherein the bilirubin is present at aconcentration of from 0.25 μM to 1.75 μM.10. The method according to any one of 1-9, wherein the period of timeis from 200 seconds to 1500 seconds.11. The method according to 10, wherein the period of time is 600seconds.12. The method according to any one of 1-11, wherein the samplecomprises a reducing agent.13. The method according to 12, wherein the reducing agent isglutathione or a derivative thereof.14. The method according to any one of 12-13, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.

Methods for Characterizing the Antimicrobial Susceptibility

1. A method of determining antimicrobial susceptibility of amicroorganism to an antimicrobial agent, the method comprising:

irradiating a plurality of samples with a monochromatic light source,each sample comprising a microorganism and an antimicrobial agent, overa plurality of intensities by the monochromatic light source for aperiod of time, and determining a rate of change in the intensity ofResonant Raman scattering for each irradiated sample, wherein eachsample comprises the same concentration of microorganism and differentconcentrations of antimicrobial agent;

calculating a net signal for each sample by comparing a normalized rateof change in the intensity of Resonant Raman scattering for each samplewith a normalized rate of change in the irradiation intensity of eachsample by the monochromatic light source; and

determining the susceptibility of the microorganism to the antimicrobialagent based on the calculated net signals of the plurality of samples.

2. The method according to 1, further comprising comparing thecalculated net signal for each sample.3. The method according to 2, wherein comparing comprises plotting thecalculated net signal for each sample as a function of the log of theconcentration of antimicrobial agent in each sample.4. The method according to any one of 2-3, further comprisingdetermining the concentration of antimicrobial agent that exhibits adecrease in the net signal.5. The method according to 4, further comprising determining theconcentration of antimicrobial agent that exhibits an increase in thenet signal.6. The method according to 1, further comprising determining metabolicactivity of the microorganism in each sample based on the calculated netsignal for each sample.7. The method according to 6, further comprising determining theconcentration of antimicrobial agent that exhibits a decrease inmetabolic activity.8. The method according to 6, further comprising determining theconcentration of antimicrobial agent that exhibits an increase inmetabolic activity.9. The method according to any one of 1-8, wherein each sample comprisesa concentration of microorganism of 10 colony forming units (CFU) ormore.10. The method according to 9, wherein each sample comprises aconcentration of microorganism of 14 CFU or more.11. The method according to 9, wherein the method comprises aliquotingeach sample from a microorganism composition having a concentration ofmicroorganism of 100 colony forming units (CFU) or more.12. The method according to any one of 1-11, wherein the concentrationof antimicrobial agent in the plurality of samples ranges from aconcentration that is below the minimum inhibitory concentration of theantimicrobial agent to a concentration that is greater than the minimumbactericidal concentration of the antimicrobial agent.13. The method according to any one of 1-12, further comprisingincubating the antimicrobial agent with the microorganism for apredetermined period of time before irradiating the sample.14. The method according to 13, wherein the antimicrobial agent isincubated with the microorganism for 10 minutes or more.15. The method according to 13, wherein the antimicrobial agent isincubated with the microorganism for 20 minutes or more.16. The method according to any one of 1-15, wherein the samplecomprises a reducing agent.17. The method according to 16, wherein the reducing agent isglutathione or a derivative thereof.18. The method according to any one of 16-17, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.19. The method according to any one of 1-18, wherein the sample isirradiated in a sample container.20. The method according to 19, wherein the sample container is a glassvial.21. The method according to 20, wherein the glass vial comprises wallshaving a zwitterionic coating.22. The method according to 21, wherein the glass vial comprises wallshaving a zwitterionic silane coating.23. The method according to any one of claims 19-22, wherein the sampleis irradiated at an interface between the sample and the container wall.24. The method according to 23, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.25. The method according to 24, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.26. The method according to 24, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.27. The method according to any one of 24-27, wherein the monochromaticlight source is focused with a collimating lens.

Methods for Phenotyping an Unknown Microorganism

1. A method of characterizing a phenotype of a microorganism, the methodcomprising:

irradiating with a monochromatic light source a sample comprising amicroorganism, a crosslinking agent and an albumin protein over aplurality of intensities by the monochromatic light source for a periodof time and determining a rate of change in the intensity of ResonantRaman scattering;

calculating a net signal for the sample by comparing a normalized rateof change in the intensity of Resonant Raman scattering for the samplewith a normalized rate of change in the irradiation intensity of thesample by the monochromatic light source; and

determining crosslink cleavage based on the calculated net signal of thesample, wherein the extent of crosslink cleavage is indicative of thephenotype of the microorganism.

2. The method according to 1, wherein the crosslinking agent is adisulfide crosslinker.3. The method according to any one of 1-2, wherein the crosslinkingagent is a glutamic acid derivative.4. The method according to 3, wherein the crosslinking agent comprises acompound of Formula (I):

5. The method according to any one of 1-4, wherein the crosslinkingagent is present in the sample in an amount such that the molar ratio ofcrosslinking agent to albumin protein is from 1:10 to 10:1.6. The method according to 5, wherein the crosslinking agent is presentin the sample in an amount such that the molar ratio of crosslinkingagent to albumin protein is about 1:2.7. The method according any one of 1-6, wherein an increase over time inthe calculated net signal of the sample is indicative that themicroorganism produces a metabolite that cleaves one or more crosslinksin the albumin protein.8. The method according to any one of 1-7, wherein the monochromaticlight source is a laser.9. The method according to 8, wherein the laser is a solid-state laserthat irradiates at 532 nm.10. The method according to any one of 1-9, wherein the sample comprisesa hydrophobic compound and an albumin protein.11. The method according to 10, wherein the hydrophobic compound is acarotenoid.12. The method according to 11, wherein the hydrophobic compound islycopene.13. The method according to any one of 10-12, wherein the hydrophobiccompound is non-covalently associated with the albumin protein.14. The method according to any one of 1-13, wherein the samplecomprises a reducing agent.15. The method according to 14, wherein the reducing agent isglutathione or a derivative thereof.16. The method according to any one of 14-15, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.17. The method according to any one of 1-16, wherein the sample isirradiated in a sample container.18. The method according to 17, wherein the sample container is a glassvial.19. The method according to 18, wherein the glass vial comprises wallshaving a zwitterionic coating.20. The method according to 19, wherein the glass vial comprises wallshaving a zwitterionic silane coating.21. The method according to any one of 17-20, wherein the sample isirradiated at an interface between the sample and the container wall.22. The method according to 21, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.23. The method according to 22, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.24. The method according to 22, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.25. The method according to any one of 22-24, wherein the monochromaticlight source is focused with a collimating lens.

Methods for Detecting a Microorganism in a Sample Using Fluorescence

1. A method for determining the presence of a microorganism in a sample,the method comprising:

irradiating a sample with a monochromatic light source for a period oftime and detecting fluorescence from the sample over the period of time;

calculating a rate of change of the fluorescence due to the presence ofa microorganism by comparing a normalized rate of change in theintensity of the detected fluorescence produced by the sample with anormalized rate of change of fluorescence produced by a control; and

determining the presence of a microorganism in the sample based on thecalculated changes in the fluorescence of the sample compared to presetthresholds.

2. The method according to 1, comprising irradiating the sample over aplurality of intensities with the monochromatic light source.3. The method according to any one of 1-2, wherein fluorescence producedby the sample and the control is detected from 2500 cm⁻¹ to 3500 cm⁻¹.4. The method according to 3, wherein fluorescence produced by thesample and the control is detected at 3000 cm⁻¹.5. The method according to any one of 1-4, wherein the control is acomposition that does not include a microorganism.6. The method according to any one of 1-5, wherein the microorganism isa pathogenic microorganism.7. The method according to any one of 1-6, wherein the monochromaticlight source is a laser.8. The method according to any one of 1-7, wherein the sample comprisesa hydrophobic compound non-covalently associated with an albuminprotein.9. The method according to any one of 1-8, further comprising a freeradical scavenger.10. The method according to 9, wherein the free radical scavengercomprises bilirubin or a derivative thereof.11. The method according to 10, wherein the bilirubin or derivativethereof is present at a concentration of from 0.5 μM to 2 μM.12. The method according to 11, wherein the bilirubin is present at aconcentration of from 0.25 μM to 1.75 μM.13. The method according to any one of 1-12, wherein the samplecomprises a reducing agent.14. The method according to 13, wherein the reducing agent isglutathione or a derivative thereof.15. The method according to any one of 13-14, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.16. The method according to any one of 1-15, wherein the sample isirradiated in a sample container.17. The method according to 16, wherein the sample container is a glassvial.18. The method according to 17, wherein the glass vial comprises wallshaving a zwitterionic coating.19. The method according to 18, wherein the glass vial comprises wallshaving a zwitterionic silane coating.20. The method according to any one of 17-19, wherein the sample isirradiated at an interface between the sample and the container wall.21. The method according to 20, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.22. The method according to 20, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.23. The method according to 22, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.24. The method according to any one of 21-23, wherein the monochromaticlight source is focused with a collimating lens.25. The method according to any one of 1-24, wherein the control is acomposition that has the same components as the sample in the absence ofmicroorganism.

Methods for Characterizing the Antimicrobial Susceptibility

1. A method of determining antimicrobial susceptibility of microorganismto an antimicrobial agent, the method comprising:

irradiating a plurality of samples with a monochromatic light source,each sample comprising a microorganism and an antimicrobial agent, for aperiod of time and detecting fluorescence from each of the irradiatedsamples over the period of time, wherein each sample comprises the sameconcentration of microorganism and different concentrations ofantimicrobial agent;

calculating a rate of change of the fluorescence in each sample bycomparing a normalized rate of change in the intensity of the detectedfluorescence produced by each sample with a normalized rate of change offluorescence produced by a control; and

determining the susceptibility of the microorganism to the antimicrobialagent based on the calculated rate of change of the fluorescence of theplurality of samples.

2. The method according to 1, further comprising comparing thecalculated rate of change of fluorescence for each sample.3. The method according to 2, wherein comparing comprises plotting thecalculated rate of change of fluorescence for each sample as a functionof the log of the concentration of antimicrobial agent in each sample.4. The method according to any one of 2-3, further comprisingdetermining the concentration of antimicrobial agent that exhibits adecrease in the rate of change of fluorescence.5. The method according to 4, further comprising determining theconcentration of antimicrobial agent that exhibits an increase in therate of change of fluorescence.6. The method according to 1, further comprising determining metabolicactivity of the microorganism in each sample based on the calculatedrate of change of fluorescence for each sample.7. The method according to 6, further comprising determining theconcentration of antimicrobial agent that exhibits a decrease inmetabolic activity.8. The method according to 6, further comprising determining theconcentration of antimicrobial agent that exhibits an increase inmetabolic activity.9. The method according to any one of 1-8, wherein each sample comprisesa concentration of microorganism of 10 colony forming units (CFU) ormore.10. The method according to 9, wherein each sample comprises aconcentration of microorganism of 14 CFU or more.11. The method according to 9, wherein the method comprises aliquotingeach sample from a microorganism composition having a concentration ofmicroorganism of 100 colony forming units (CFU) or more.12. The method according to any one of 1-11, wherein the concentrationof antimicrobial agent in the plurality of samples ranges from aconcentration that is below the minimum inhibitory concentration of theantimicrobial agent to a concentration that is greater than the minimumbactericidal concentration of the antimicrobial agent.13. The method according to any one of 1-12, further comprisingincubating the antimicrobial agent with the microorganism for apredetermined period of time before irradiating the sample.14. The method according to 13, wherein the antimicrobial agent isincubated with the microorganism for 10 minutes or more.15. The method according to 13, wherein the antimicrobial agent isincubated with the microorganism for 20 minutes or more.16. The method according to any one of 1-15, wherein the samplecomprises a reducing agent.17. The method according to 16, wherein the reducing agent isglutathione or a derivative thereof.18. The method according to any one of 16-17, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.19. The method according to any one of 1-18, wherein the sample isirradiated in a sample container.20. The method according to 19, wherein the sample container is a glassvial.21. The method according to 20, wherein the glass vial comprises wallshaving a zwitterionic coating.22. The method according to 21, wherein the glass vial comprises wallshaving a zwitterionic silane coating.23. The method according to any one of 19-22, wherein the sample isirradiated at an interface between the sample and the container wall.24. The method according to 23, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.25. The method according to 24, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.26. The method according to 24, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.27. The method according to any one of 24-27, wherein the monochromaticlight source is focused with a collimating lens.28. The method according to any one of 1-27, wherein fluorescenceproduced by the sample and the control is detected from 2500 cm⁻¹ to3500 cm⁻¹.29. The method according to 28, wherein fluorescence produced by thesample and the control is detected at 3000 cm⁻¹.30. The method according to any one of 1-29, wherein the control is acomposition that does not include a microorganism.31. The method according to any one of 1-30, wherein the control is acomposition that has the same components as the sample in the absence ofmicroorganism.32. The method according to any one of 1-31, comprising irradiating eachsample over a plurality of intensities with the monochromatic lightsource.

Methods for Phenotyping an Unknown Microorganism

1. A method of characterizing a phenotype of a microorganism, the methodcomprising:

irradiating with a monochromatic light source, a sample comprising amicroorganism, a crosslinking agent and an albumin protein, for a periodof time and detecting fluorescence from the sample over the period oftime;

calculating a rate of change of the fluorescence by comparing anormalized rate of change in the intensity of the detected fluorescenceproduced by the sample with a normalized rate of change of fluorescenceproduced by a control; and

determining crosslink cleavage based on the calculated rate of change offluorescence of the sample, wherein the extent of crosslink cleavage isindicative of the phenotype of the microorganism.

2. The method according to 1, wherein the crosslinking agent is adisulfide crosslinker.3. The method according to any one of 1-2, wherein the crosslinkingagent is a glutamic acid derivative.4. The method according to 3, wherein the crosslinking agent comprises acompound of Formula (I):

5. The method according to any one of 1-4, wherein the crosslinkingagent is present in the sample in an amount such that the molar ratio ofcrosslinking agent to albumin protein is from 1:10 to 10:1.

6. The method according to 5, wherein the crosslinking agent is presentin the sample in an amount such that the molar ratio of crosslinkingagent to albumin protein is about 1:2.7. The method according any one of 1-6, wherein an increase in thecalculated rate of change in the fluorescence of the sample isindicative that the microorganism produces a metabolite that cleaves oneor more crosslinks in the albumin protein.8. The method according to any one of 1-7, wherein the monochromaticlight source is a laser.9. The method according to 8, wherein the laser is a solid-state laserthat irradiates at 532 nm.10. The method according to any one of 1-9, wherein the sample comprisesa hydrophobic compound and an albumin protein.11. The method according to 10, wherein the hydrophobic compound is acarotenoid.12. The method according to 11, wherein the hydrophobic compound islycopene.13. The method according to any one of 10-12, wherein the hydrophobiccompound is non-covalently associated with the albumin protein.14. The method according to any one of 1-13, wherein the samplecomprises a reducing agent.15. The method according to 14, wherein the reducing agent isglutathione or a derivative thereof.16. The method according to any one of 14-15, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.17. The method according to any one of 1-16, wherein the sample isirradiated in a sample container.18. The method according to 17, wherein the sample container is a glassvial.19. The method according to 18, wherein the glass vial comprises wallshaving a zwitterionic coating.20. The method according to 19, wherein the glass vial comprises wallshaving a zwitterionic silane coating.21. The method according to any one of 17-20, wherein the sample isirradiated at an interface between the sample and the container wall.22. The method according to 21, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.23. The method according to claim 22, wherein the monochromatic lightsource is focused in the sample at a position of from 0.01 mm to 2 mmfrom the surface of the container wall.24. The method according to 22, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.25. The method according to any one of 22-24, wherein the monochromaticlight source is focused with a collimating lens.26. The method according to any one of 1-25, wherein fluorescenceproduced by the sample and the control is detected from 2500 cm⁻¹ to3500 cm⁻¹.27. The method according to 26, wherein fluorescence produced by thesample and the control is detected at 3000 cm⁻¹.28. The method according to any one of 1-27, wherein the control is acomposition that does not include a microorganism.29. The method according to any one of 1-28, wherein the control is acomposition that has the same components as the sample in the absence ofmicroorganism.30. The method according to any one of 1-29, comprising irradiating eachsample over a plurality of intensities with the monochromatic lightsource.

Systems for Resonant Raman Spectroscopy

1. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory comprises instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate a sample with a monochromatic light source at a first        irradiation intensity and a second irradiation intensity;    -   determine the intensity of Resonant Raman scattering at the        first irradiation intensity and the second irradiation        intensity;    -   calculate a rate of change of the intensity of Resonant Raman        scattering in response to the change in irradiation intensity        from the first irradiation intensity to the second irradiation        intensity; and    -   compare the rate of change in the intensity of Resonant Raman        scattering with the rate of change in the irradiation intensity        by the monochromatic light source to determine the changes to        Resonant Raman response of the sample.        2. The system according to 1, wherein the monochromatic light        source is a laser.        3. The system according to 2, wherein the laser is a Nd:YAG        laser.        4. The system according to 3, wherein the laser is a        frequency-doubled Nd:YAG laser.        5. The system according to any one of 1-4, wherein the detector        is a charged coupled device (CCD) detector.        6. The system according to any one of 1-5, wherein the memory        further comprises instructions, which when executed by the        processor, cause the processor to irradiate the sample over a        plurality of intensities by the monochromatic light source over        a period of time and determine a rate of change in the intensity        of Resonant Raman scattering.        7. The system according to any one of 1-6, wherein the memory        further comprises instructions which when executed by the        processor, cause the processor to:

irradiate a first sample over a plurality of intensities by themonochromatic light source for a period of time and determine a rate ofchange in the intensity of Resonant Raman scattering for the firstsample;

calculate a net signal of the first sample by comparing a normalizedrate of change in the intensity of Resonant Raman scattering for thefirst sample with a normalized rate of change in the irradiationintensity of the first sample by the monochromatic light source;

irradiate a second sample over a plurality of intensities by themonochromatic light source for the period of time and determine a rateof change in the intensity of Resonant Raman scattering for the secondsample; and

calculate a net signal of the second sample by comparing a normalizedrate of change in the intensity of Resonant Raman scattering for thesecond sample with a normalized rate of change in the irradiationintensity of the second sample by the monochromatic light source.

8. The system according to 7, wherein the memory further comprisesinstructions which when executed by the processor, cause the processorto determine that the first sample comprises a different gaseouscomposition from the second sample based on the compared calculated netsignals.9. The system according to 8, wherein the memory further comprisesinstructions which when executed by the processor, cause the processorto determine that the first sample or the second sample comprisesactively metabolizing microorganisms based on the compared calculatednet signals.

Systems for Detecting a Microorganism in a Sample

1. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory includes instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate a sample over one or more intensities by a        monochromatic light source for a period of time and calculate a        rate of change in the intensity of Resonant Raman scattering for        the sample;    -   calculate a net signal of the sample by comparing a normalized        rate of change in the intensity of Resonant Raman scattering for        the sample with a normalized rate of change in the irradiation        intensity of the sample by the monochromatic light source; and    -   determine the presence or absence of a microorganism in the        sample based on the calculated net signal of the sample.        2. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine that a microorganism is present        when the calculated net signal of the sample is above a        predetermined threshold.        2. The system according to 2, wherein the predetermined        threshold is a net signal of 1.        3. The system according to any one of 1-2, wherein the        monochromatic light source is a laser.        4. The system according to 3, wherein the laser is a solid-state        laser that irradiates at 532 nm.        5. The system according to any one of 1-4, wherein the sample        comprises a hydrophobic compound non-covalently associated with        an albumin protein.        6. The system according to any one of 1-5, wherein the sample        comprises a reducing agent.        7. The system according to 6, wherein the reducing agent is        glutathione or a derivative thereof.        8. The system according to any one of 6-7, wherein the reducing        agent is present in the sample at a concentration of 0.1 mg/mL        to 1 mg/mL.        9. The system according to any one of 1-8, further comprising a        free radical scavenger.        10. The system according to 9, wherein the free radical        scavenger comprises bilirubin or a derivative thereof.        11. The system according to 10, wherein the bilirubin or        derivative thereof is present at a concentration of from 0.5 μM        to 2 μM.        12. The system according to 11, wherein the bilirubin is present        at a concentration of from 0.25 μM to 1.75 μM.        13. The system according to any one of 1-12, wherein the        detector is a charge couple device (CCD) detector.        14. The system according to any one of 1-13, wherein further        comprising a sample container.        15. The system according to 14, wherein the sample container is        a glass vial.        16. The system according to 15, wherein the glass vial comprises        walls having a zwitterionic coating.        17. The system according to 16, wherein the glass vial comprises        walls having a zwitterionic silane coating.        18. The system according to any one of 14-17, wherein the system        is configured to irradiate the sample at an interface between        the sample and the container wall.        19. The system according to 18, wherein the monochromatic light        source is focused at a position at the interface between the        sample and the container wall.        20. The system according to 19, wherein the monochromatic light        source is focused in the sample at a position of from 0.01 mm to        2 mm from the surface of the container wall.        21. The system according to 20, wherein the monochromatic light        source is focused in the sample at a position of about 0.2 mm        from the surface of the container wall.        22. The system according to any one of 19-21, wherein the        monochromatic light source is focused with a collimating lens.        23. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory includes instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate a first sample over a plurality of intensities by a        monochromatic light source for a period of time and calculate a        rate of change in the intensity of Resonant Raman scattering for        the first sample;    -   calculate a net signal of the first sample by comparing a        normalized rate of change in the intensity of Resonant Raman        scattering for the first sample with a normalized rate of change        in the irradiation intensity of the first sample by the        monochromatic light source;    -   irradiate a second sample over a plurality of intensities by the        monochromatic light source for the period of time and determine        a rate of change in the intensity of Resonant Raman scattering        for the second sample;    -   calculate a net signal of the second sample by comparing a        normalized rate of change in the intensity of Resonant Raman        scattering for the second sample with a normalized rate of        change in the irradiation intensity of the second sample by the        monochromatic light source; and    -   determine the presence or absence of a microorganism in one or        more of the first sample or the second sample by comparing the        net signal of the first sample with the net signal of the second        sample.        24. The system according to 23, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine that a microorganism is present        in the second sample when the calculated net signal of the        second sample is greater than the calculated net signal of the        first sample.        25. The system according to 24, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine that a microorganism is present        in the first sample when the calculated net signal of the first        sample is greater than the calculated net signal of the second        sample.        26. The system according to any one of 23-25, wherein the        monochromatic light source is a laser.        27. The system according to 26, wherein the laser is a        solid-state laser that irradiates at 532 nm.        28. The system according to any one of 23-27, wherein the sample        comprises a hydrophobic compound non-covalently associated with        an albumin protein.        29. The system according to any one of 23-28, wherein the sample        comprises a reducing agent.        30. The system according to 29, wherein the reducing agent is        glutathione or a derivative thereof.        31. The system according to any one of 29-30, wherein the        reducing agent is present in the sample at a concentration of        0.1 mg/mL to 1 mg/mL.        32. The system according to any one of 23-31, further comprising        a free radical scavenger.        33. The system according to 32, wherein the free radical        scavenger comprises bilirubin or a derivative thereof.        34. The system according to 33, wherein the bilirubin or        derivative thereof is present at a concentration of from 0.5 μM        to 2 μM.        35. The system according to 33, wherein the bilirubin is present        at a concentration of from 0.25 μM to 1.75 μM.        36. The system according to any one of 70-79, wherein the        detector is a charge couple device (CCD) detector.        37. The system according to any one of 23-36, further comprising        a sample container.        38. The system according to 37, wherein the sample container is        a glass vial.        39. The system according to 38, wherein the glass vial comprises        walls having a zwitterionic coating.        40. The system according to 39, wherein the glass vial comprises        walls having a zwitterionic silane coating.        41. The system according to any one of 37-40, wherein the system        is configured to irradiate the sample at an interface between        the sample and the container wall.        42. The system according to 41, wherein the monochromatic light        source is focused at a position at the interface between the        sample and the container wall.        43. The system according to 42, wherein the monochromatic light        source is focused in the sample at a position of from 0.01 mm to        2 mm from the surface of the container wall.        44. The system according to 42, wherein the monochromatic light        source is focused in the sample at a position of about 0.2 mm        from the surface of the container wall.        45. The system according to any one of 42-44, wherein the        monochromatic light source is focused with a collimating lens.        46. A system comprising:

(a) a monochromatic light source;

(b) an optical adjustment component;

(c) a photodetector; and

(d) a processor comprising memory operably coupled to the processorwherein the memory comprises instructions stored thereon, which whenexecuted by the processor, cause the processor to:

irradiate a sample in a sample holder with the monochromatic lightsource at a first irradiation intensity and a second irradiationintensity for preset durations;

measure scattered light from the sample with the photodetector;

determine the intensity of Resonant Raman scattering and fluorescencescattering at the first irradiation intensity and the second irradiationintensity;

-   -   calculate a rate of change in the intensity of Resonant Raman        scattering and the intensity of fluorescence scattering; and    -   correct the rate of change of the intensity of Resonant Raman        scattering and the intensity of fluorescence scattering to        obtain a net signal.        47. The system according to 46, wherein the optical adjustment        component comprises collimating optics mounted on a linear table        that is configured to produce an adjustable focal spot.        48. The system according to 46, wherein the optical adjustment        component comprises a mechanical shutter.        49. The system according to 46, further comprising a rotary        table with a plurality of sample chambers.        50. The system according to 49, wherein the rotary table        comprises 8 sample chambers.        51. The system according to 50, further comprising a subsystem        for characterizing incoherently scattered light, wherein the        subsystem comprises:

collimating optics; and

optical adjustment components configured to spread the incoherentlyscattered light onto a linear array of photodetectors.

52. The system according to 51, wherein the processor further comprisesmemory with instructions stored thereon, which when executed by theprocessor, cause the processor to move the collimating optics to focuslight on each of the sample chambers.53. The system according to 46, wherein the sample comprises an albuminwith an incorporated ligand.54. The system according to 1, wherein the memory further comprisesinstructions which when executed by the processor, cause the processorto:

determine a rate of change in the intensity of fluorescent scatteringfrom a standard reference sample;

calculate a net signal as the rate of change in the intensity of theResonant Raman scattering minus the rate of change in the intensity offluorescent scattering from the standard sample.

55. The system according to 53 or 54, wherein the memory furthercomprises instructions which when executed by the processor, cause theprocessor to:

determine a rate of change in total output from a standard referencesample;

calculate a net signal as the rate of change in the intensity of theResonant Raman scattering minus the rate of change in the intensity ofResonant Raman scattering from the standard sample.

56. The system according to 53 or 54, wherein the memory furthercomprises instructions which when executed by the processor, cause theprocessor to compare the net signal with preset thresholds, and todetermine that the first sample includes actively metabolizingmicroorganisms based on the comparison.57. The system according to 46, wherein the sample comprises a reducingagent.58. The system according to 57, wherein the sample comprises a disulfidecrosslinking agent.59. The system according to 58, where the disulfide crosslinking agentcomprises a core that is cleaved by enzymes or a metabolite produced bythe microorganism in the sample.60. The method according to 59, wherein the crosslinking agent comprisesa compound of Formula (I):

61. The system according to 46, wherein the sample holder is a glassvial.62. The system according to 46, wherein the sample holder comprises acoating that modifies albumin absorption.63. The system according to claim 62, wherein the coating comprises aZwitterionic coating64. The system according to 46, wherein the processor is configured toexpose the sample to the monochromatic light source to minimize the netsignal.65. The system according to 46, wherein the system is configured toirradiate the sample at an interface between the sample and a surface ofthe sample holder.66. The system according to 65, wherein the system is configured tomaximize the net signal.

Systems for Correcting for Drifts in Laser Power During Non-Linear RamanSpectroscopy

1. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory includes instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate a reference composition over a plurality of        intensities by the monochromatic light source for the period of        time and determine a rate of change in the intensity of Resonant        Raman scattering, wherein the reference composition comprises a        reference compound that exhibits no change in the intensity of        Resonant Raman scattering in response to the change in        irradiation intensity by the monochromatic light source; and    -   calculate a net signal of the reference composition by comparing        the rate of change in the intensity of Resonant Raman scattering        for the reference composition with the rate of change in the        irradiation intensity of the reference composition by the        monochromatic light source to determine if the monochromatic        light source exhibits thermal drift.        2. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to:

irradiate a sample over a range of intensities by a monochromatic lightsource for a period of time and determine a rate of change in theintensity of Resonant Raman scattering;

multiply the net signal of the reference composition with the rate ofchange of irradiation intensity of the sample by the monochromatic lightsource to produce a correction factor; and

subtract the correction factor from the determined rate of change in theintensity of Resonant Raman scattering for the sample to correct for thethermal drift of the monochromatic light source.

3. The system according to any one of 1-2, wherein the monochromaticlight source is a laser.4. The system according to 3, wherein the laser is a solid-state laserthat irradiates at 532 nm.5. The system according to any one of 1-4, wherein the sample comprisesa hydrophobic compound non-covalently associated with an albuminprotein.6. The system according to any one of 1-5, wherein the sample comprisesa reducing agent.7. The system according to 6, wherein the reducing agent is glutathioneor a derivative thereof.8. The system according to any one of 6-7, wherein the reducing agent ispresent in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.9. The system according to any one of 1-8, further comprising a freeradical scavenger.10. The system according to 9, wherein the free radical scavengercomprises bilirubin or a derivative thereof.11. The system according to 10, wherein bilirubin or derivative thereofis present at a concentration of from 0.5 μM to 2 μM.12. The system according to 10, wherein the bilirubin is present at aconcentration of from 0.25 μM to 1.75 μM.13. The system according to any one of 1-12, wherein the period of timeis from 200 seconds to 1500 seconds.14. The system according to 13, wherein the period of time is 600seconds.15. The system according to any one of 1-14, wherein the detector is acharge couple device (CCD) detector.

Systems for Characterizing the Antimicrobial Susceptibility

1. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory comprises instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate a plurality of samples, each sample comprising a        microorganism and an antimicrobial agent over a plurality of        intensities by the monochromatic light source for a period of        time and determine a rate of change in the intensity of Resonant        Raman scattering for each irradiated sample, wherein each sample        comprises the same concentration of microorganism and different        concentrations of antimicrobial agent;    -   calculate a net signal for each sample by comparing a normalized        rate of change in the intensity of Resonant Raman scattering for        each sample with a normalized rate of change in the irradiation        intensity of each sample by the monochromatic light source; and    -   determine the susceptibility of the microorganism to the        antimicrobial agent based on the calculated net signals the        plurality of samples.        2. The system according to 1, wherein the memory comprises        instructions stored thereon, which when executed by the        processor, cause the processor to compare the calculated net        signal for each sample.        3. The system according to 2, wherein the memory comprises        instructions stored thereon, which when executed by the        processor, cause the processor to plot the calculated net signal        for each sample as a function of the log of the concentration of        antimicrobial agent in each sample.        4. The system according to any one of 2-3, wherein the memory        comprises instructions stored thereon, which when executed by        the processor, cause the processor to determine the        concentration of antimicrobial agent that exhibits a decrease in        the net signal.        5. The system according to 4, wherein the memory comprises        instructions stored thereon, which when executed by the        processor, cause the processor to determine the concentration of        antimicrobial agent that exhibits an increase in the net signal.        6. The system according to 1, wherein the memory comprises        instructions stored thereon, which when executed by the        processor, cause the processor to determine metabolic activity        of the microorganism in each sample based on the calculated net        signal for each sample.        7. The system according to 6, wherein the memory comprises        instructions stored thereon, which when executed by the        processor, cause the processor to determine the concentration of        antimicrobial agent that exhibits a decrease in metabolic        activity.        8. The system according to 6, wherein the memory comprises        instructions stored thereon, which when executed by the        processor, cause the processor to determine the concentration of        antimicrobial agent that exhibits an increase in metabolic        activity.        9. The system according to any one of 1-8, wherein each sample        comprises a concentration of microorganism of 10 colony forming        units (CFU) or more.        10. The system according to 9, wherein each sample comprises a        concentration of microorganism of 14 CFU or more.        11. The system according to any one of 1-10, wherein the        concentration of antimicrobial agent in the plurality of samples        ranges from a concentration that is below the minimum inhibitory        concentration of the antimicrobial agent to a concentration that        is greater than the minimum bactericidal concentration of the        antimicrobial agent.        12. The system according to any one of 1-11, wherein the sample        comprises a reducing agent.        13. The system according to 12, wherein the reducing agent is        glutathione or a derivative thereof.        14. The system according to any one of 12-13, wherein the        reducing agent is present in the sample at a concentration of        0.1 mg/mL to 1 mg/mL.        15. The system according to any one of 1-14, wherein further        comprising a sample container.        16. The system according to 15, wherein the sample container is        a glass vial.        17. The system according to 16, wherein the glass vial comprises        walls having a zwitterionic coating.        18. The system according to 17, wherein the glass vial comprises        walls having a zwitterionic silane coating.        19. The system according to any one of 15-18, wherein the system        is configured to irradiate the sample at an interface between        the sample and the container wall.        20. The system according to 19, wherein the monochromatic light        source is focused at a position at the interface between the        sample and the container wall.        21. The system according to 20, wherein the monochromatic light        source is focused in the sample at a position of from 0.01 mm to        2 mm from the surface of the container wall.        22. The system according to 20, wherein the monochromatic light        source is focused in the sample at a position of about 0.2 mm        from the surface of the container wall.        23. The system according to any one of 20-22, wherein the        monochromatic light source is focused with a collimating lens.        24. The system according to any one of 1-23, wherein the        detector is a charge couple device (CCD) detector.

Systems for Phenotyping an Unknown Microorganism

1. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory comprises instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate with a monochromatic light source a sample comprising        a microorganism, a crosslinking agent and an albumin protein        over a plurality of intensities by the monochromatic light        source for a period of time and determine a rate of change in        the intensity of Resonant Raman scattering;    -   calculate a net signal for the sample by comparing a normalized        rate of change in the intensity of Resonant Raman scattering for        the sample with a normalized rate of change in the irradiation        intensity of the sample by the monochromatic light source; and    -   determine crosslink cleavage based on the calculated net signal        of the sample, wherein the extent of crosslink cleavage is        indicative of the phenotype of the microorganism.        2. The system according to 1, wherein the crosslinking agent is        a disulfide crosslinker.        3. The system according to any one of 1-2, wherein the        crosslinking agent is a glutamic acid derivative.        4. The system according to 3, wherein the crosslinking agent        comprises a compound of Formula (I):

5. The system according to any one of 1-4, wherein the crosslinkingagent is present in the sample in an amount such that the molar ratio ofcrosslinking agent to albumin protein is from 1:10 to 10:1.6. The system according to 5, wherein the crosslinking agent is presentin the sample in an amount such that the molar ratio of crosslinkingagent to albumin protein is about 1:2.7. The system according any one of 1-6, wherein an increase over time inthe calculated net signal of the sample is indicative that themicroorganism produces a metabolite that cleaves one or more crosslinksin the albumin protein.8. The system according to any one of 1-7, wherein the monochromaticlight source is a laser.9. The system according to 8, wherein the laser is a solid-state laserthat irradiates at 532 nm.10. The system according to any one of 1-9, wherein the sample comprisesa hydrophobic compound and an albumin protein.11. The system according to 10, wherein the hydrophobic compound is acarotenoid.12. The system according to 11, wherein the hydrophobic compound islycopene.13. The system according to any one of 10-12, wherein the hydrophobiccompound is non-covalently associated with the albumin protein.14. The system according to any one of 1-13, wherein the samplecomprises a reducing agent.15. The system according to 14, wherein the reducing agent isglutathione or a derivative thereof.16. The system according to any one of 14-15, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.17. The system according to any one of 1-16, further comprising a samplecontainer.18. The system according to 17, wherein the sample container is a glassvial.19. The system according to 18, wherein the glass vial comprises wallshaving a zwitterionic coating.20. The system according to 19, wherein the glass vial comprises wallshaving a zwitterionic silane coating.21. The system according to any one of 17-20, wherein the system isconfigured to irradiate the sample at an interface between the sampleand the container wall.22. The system according to 21, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.23. The system according to 22, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.24. The system according to 22, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.25. The system according to any one of 22-24, wherein the monochromaticlight source is focused with a collimating lens.26. The system according to any one of 1-25, wherein the detector is acharge couple device (CCD) detector.

Systems for Detecting a Microorganism in a Sample Via Fluorescence

1. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory includes instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate a sample by a monochromatic light source for a period        of time and detect fluorescence from the sample over the period        of time;    -   calculate a rate of change of the fluorescence due to the        presence of microorganisms by comparing a normalized rate of        change in the intensity of the detected fluorescence produced by        the sample with a normalized rate of change in fluorescence from        a control; and    -   determine the presence or absence of a microorganism in the        sample based on the calculated rate of change of fluorescence of        the sample.        2. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine that a microorganism is present        when the calculated rate of change of fluorescence is above a        predetermined threshold.        3. The system according to any one of 1-2, wherein the        monochromatic light source is a laser.        4. The system according to 3, wherein the laser is a solid-state        laser that irradiates at 532 nm.        5. The system according to any one of 1-4, wherein the sample        comprises a hydrophobic compound non-covalently associated with        an albumin protein.        6. The system according to any one of 1-5, wherein the sample        comprises a reducing agent.        7. The system according to 6, wherein the reducing agent is        glutathione or a derivative thereof.        8. The system according to any one of 6-7, wherein the reducing        agent is present in the sample at a concentration of 0.1 mg/mL        to 1 mg/mL.        9. The system according to any one of 1-8, wherein the detector        is a charge couple device (CCD) detector.        10. The system according to any one of 1-9, wherein further        comprising a sample container.        11. The system according to 10, wherein the sample container is        a glass vial.        12. The system according to 11, wherein the glass vial comprises        walls having a zwitterionic coating.        13. The system according to 12, wherein the glass vial comprises        walls having a zwitterionic silane coating.        14. The system according to any one of 11-13, wherein the system        is configured to irradiate the sample at an interface between        the sample and the container wall.        15. The system according to 14, wherein the monochromatic light        source is focused at a position at the interface between the        sample and the container wall.        16. The system according to 15, wherein the monochromatic light        source is focused in the sample at a position of from 0.01 mm to        2 mm from the surface of the container wall.        17. The system according to 16, wherein the monochromatic light        source is focused in the sample at a position of about 0.2 mm        from the surface of the container wall.        18. The system according to any one of 15-17, wherein the        monochromatic light source is focused with a collimating lens.        19. The system according to any one of 1-18, wherein        fluorescence produced by the sample and the control is detected        from 2500 cm⁻¹ to 3500 cm⁻¹.        20. The system according to 19, wherein fluorescence produced by        the sample and the control is detected at 3000 cm⁻¹.        21. The system according to any one of 1-20, wherein the control        is a composition that does not include a microorganism.        22. The system according to any one of 1-21, wherein the        microorganism is a pathogenic microorganism.        23. The system according to any one of 1-22, wherein the control        is a composition that has the same components as the sample in        the absence of microorganism.        24. The system according to any one of 1-23, wherein the system        is configured to irradiate a sample over a plurality of        intensities with the monochromatic light source.

Systems for Characterizing the Antimicrobial Susceptibility

1. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory includes instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate a plurality of samples comprising a microorganism,        each sample comprising a microorganism and an antimicrobial        agent, with the monochromatic light source for a period of time        and detecting fluorescence from each of the irradiated samples        over the period of time, wherein each sample comprises the same        concentration of microorganism and different concentrations of        antimicrobial agent;    -   calculate a rate of change of the fluorescence in each sample by        comparing a normalized rate of change in the intensity of the        detected fluorescence produced by each sample with a normalized        rate of change of fluorescence produced by a control; and    -   determine the susceptibility of the microorganism to the        antimicrobial agent based on the calculated rate of change of        the fluorescence of the plurality of samples.        2. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to compare the calculated rate of change of        fluorescence for each sample.        3. The system according to 2, wherein comparing comprises        plotting the calculated rate of change of fluorescence for each        sample as a function of the log of the concentration of        antimicrobial agent in each sample.        4. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine the concentration of        antimicrobial agent that exhibits a decrease in the rate of        change of fluorescence.        5. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine the concentration of        antimicrobial agent that exhibits an increase in the rate of        change of fluorescence.        6. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine metabolic activity of the        microorganism in each sample based on the calculated rate of        change of fluorescence for each sample.        7. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine the concentration of        antimicrobial agent that exhibits a decrease in metabolic        activity.        8. The system according to 1, wherein the memory further        comprises instructions, which when executed by the processor,        cause the processor to determine the concentration of        antimicrobial agent that exhibits an increase in metabolic        activity.        9. The system according to any one of 1-8, wherein each sample        comprises a concentration of microorganism of 10 colony forming        units (CFU) or more.        10. The system according to 9, wherein each sample comprises a        concentration of microorganism of 14 CFU or more.        11. The system according to 9, wherein each sample is aliquoted        from a microorganism composition having a concentration of        microorganism of 100 colony forming units (CFU) or more.        12. The system according to any one of 1-11, wherein the        concentration of antimicrobial agent in the plurality of samples        ranges from a concentration that is below the minimum inhibitory        concentration of the antimicrobial agent to a concentration that        is greater than the minimum bactericidal concentration of the        antimicrobial agent.        13. The system according to any one of 1-12, wherein the        antimicrobial agent is incubated with the microorganism for a        predetermined period of time before irradiating the sample.        14. The system according to 13, wherein the antimicrobial agent        is incubated with the microorganism for 10 minutes or more.        15. The system according to 13, wherein the antimicrobial agent        is incubated with the microorganism for 20 minutes or more.        16. The system according to any one of 1-15, wherein the sample        comprises a reducing agent.        17. The system according to 16, wherein the reducing agent is        glutathione or a derivative thereof.        18. The system according to any one of 16-17, wherein the        reducing agent is present in the sample at a concentration of        0.1 mg/mL to 1 mg/mL.        19. The system according to any one of 1-18, wherein the sample        is irradiated in a sample container.        20. The system according to 19, wherein the sample container is        a glass vial.        21. The system according to 20, wherein the glass vial comprises        walls having a zwitterionic coating.        22. The system according to 21, wherein the glass vial comprises        walls having a zwitterionic silane coating.        23. The system according to any one of 19-22, wherein the system        is configured to irradiate the sample at an interface between        the sample and the container wall.        24. The system according to 23, wherein the monochromatic light        source is focused at a position at the interface between the        sample and the container wall.        25. The system according to 24, wherein the monochromatic light        source is focused in the sample at a position of from 0.01 mm to        2 mm from the surface of the container wall.        26. The system according to 24, wherein the monochromatic light        source is focused in the sample at a position of about 0.2 mm        from the surface of the container wall.        27. The system according to any one of 24-27, wherein the        monochromatic light source is focused with a collimating lens.        28. The system according to any one of 1-27, wherein the system        is configured to detect fluorescence produced by the sample and        the control from 2500 cm⁻¹ to 3500 cm⁻¹.        29. The system according to 28, wherein the system is configured        to detect fluorescence produced by the sample and the control at        3000 cm⁻¹.        30. The system according to any one of claims 1-29, wherein the        control is a composition that does not include a microorganism.        31. The system according to any one of 1-30, wherein the control        is a composition that has the same components as the sample in        the absence of microorganism.        32. The system according to any one of 1-31, wherein the system        is configured to irradiate each sample over a plurality of        intensities with the monochromatic light source.

Systems for Phenotyping an Unknown Microorganism

1. A system comprising:

a monochromatic light source;

a detector; and

a processor comprising memory operably coupled to the processor whereinthe memory includes instructions stored thereon, which when executed bythe processor, cause the processor to:

-   -   irradiate with a monochromatic light source a sample comprising        a microorganism, a crosslinking agent and an albumin protein for        a period of time and detect fluorescence from the sample over        the period of time;    -   calculate a rate of change of the fluorescence by comparing a        normalized rate of change in the intensity of the detected        fluorescence produced by the sample with a normalized rate of        change of fluorescence produced by a control; and    -   determine crosslink cleavage based on the calculated rate of        change of fluorescence of the sample, wherein the extent of        crosslink cleavage is indicative of the phenotype of the        microorganism.        2. The system according to 1, wherein the crosslinking agent is        a disulfide crosslinker.        3. The system according to any one of 1-2, wherein the        crosslinking agent is a glutamic acid derivative.        4. The system according to 3, wherein the crosslinking agent        comprises a compound of Formula (I):

5. The system according to any one of 1-4, wherein the crosslinkingagent is present in the sample in an amount such that the molar ratio ofcrosslinking agent to albumin protein is from 1:10 to 10:1.6. The system according to 5, wherein the crosslinking agent is presentin the sample in an amount such that the molar ratio of crosslinkingagent to albumin protein is about 1:2.7. The system according any one of 1-6, wherein an increase in thecalculated rate of change in the fluorescence of the sample causes theprocessor to indicate that the microorganism produces a metabolite thatcleaves one or more crosslinks in the albumin protein.8. The system according to any one of 1-7, wherein the monochromaticlight source is a laser.9. The system according to 8, wherein the laser is a solid-state laserthat irradiates at 532 nm.10. The system according to any one of 1-9, wherein the sample comprisesa hydrophobic compound and an albumin protein.11. The system according to 10, wherein the hydrophobic compound is acarotenoid.12. The system according to 11, wherein the hydrophobic compound islycopene.13. The system according to any one of 10-12, wherein the hydrophobiccompound is non-covalently associated with the albumin protein.14. The system according to any one of 1-13, wherein the samplecomprises a reducing agent.15. The system according to 14, wherein the reducing agent isglutathione or a derivative thereof.16. The system according to any one of 14-15, wherein the reducing agentis present in the sample at a concentration of 0.1 mg/mL to 1 mg/mL.17. The system according to any one of 1-16, wherein the system isconfigured to irradiate the sample in a sample container.18. The system according to 17, wherein the sample container is a glassvial.19. The system according to 18, wherein the glass vial comprises wallshaving a zwitterionic coating.20. The system according to 19, wherein the glass vial comprises wallshaving a zwitterionic silane coating.21. The system according to any one of 17-20, wherein the system isconfigured to irradiate the sample at an interface between the sampleand the container wall.22. The system according to 21, wherein the monochromatic light sourceis focused at a position at the interface between the sample and thecontainer wall.23. The system according to 22, wherein the monochromatic light sourceis focused in the sample at a position of from 0.01 mm to 2 mm from thesurface of the container wall.24. The system according to 22, wherein the monochromatic light sourceis focused in the sample at a position of about 0.2 mm from the surfaceof the container wall.25. The system according to any one of 22-24, wherein the monochromaticlight source is focused with a collimating lens.26. The system according to any one of 1-25, wherein the system isconfigured to detect fluorescence produced by the sample and the controlfrom 2500 cm⁻¹ to 3500 cm⁻¹.27. The system according to 26, wherein the system is configured todetect fluorescence produced by the sample and the control at 3000 cm⁻¹.28. The system according to any one of 1-27, wherein the control is acomposition that does not include a microorganism.29. The system according to any one of 1-28, wherein the control is acomposition that has the same components as the sample in the absence ofmicroorganism.30. The system according to any one of 1-29, wherein the system isconfigured to irradiate a sample over a plurality of intensities withthe monochromatic light source.

EXPERIMENTAL

As can be appreciated from the disclosure provided above, the presentdisclosure has a wide variety of applications. The following examplesare put forth so as to provide those of ordinary skill in the art with acomplete disclosure and description of how to make and use the presentinvention, and are not intended to limit the scope of the invention norare they intended to represent that the experiments below are all or theonly experiments performed. Those of skill in the art will readilyrecognize a variety of noncritical parameters that could be changed ormodified to yield essentially similar results. Efforts have been made toensure accuracy with respect to numbers used (e.g. amounts, temperature,etc.) but some experimental errors and deviations should be accountedfor.

Methods

An example of the subject methods includes a Raman spectrometer builtaround a laser whose wavelength is close to an absorption bandgap thatis affected by changes in the excited state of the molecule beingprobed. With respect to a system that comprises lycopene incorporatedinto albumin, a laser with wavelength 532 nm is used because thiswavelength is at the tail of the lycopene absorption triplet, and isaffected by changes in the excited state. The system also includes acomponent that modulates the laser intensity over time by small amounts.

Laser light at 532 nm is generated with an optical pump at 808 nm thatpumps a cavity at 1064 nm, and which is Q-switched to 532 nm in anexternal cavity. The output of the final Q-switching cavity is verysensitive to pointing direction, which in turn is very sensitive totemperature. In turn, the temperature changes with heat buildup (anddissipation) from within the cavity. Thus, changes to the currentapplied in the pump laser do not always manifest as changes in the 532nm laser light output from the external cavity.

It was found that slight changes in the temperature of the externalcavity can affect the power output from the laser, and so any mechanismthat affects this can be used to modulate the laser power. In oneembodiment, it was determined that varying the CCD shutter time (i.e.,the time used to acquire data in the CCD) affects the laser power. Inthis example, the frequency with which data is shifted out of the CCDaffects the heat buildup within the CCD, which then affects thetemperature of the external laser cavity that is in thermal proximitywith the CCD.

The subject systems were configured to measure the time dependentchanges in the Resonant Raman intensity, as the laser intensity is beingmodulated. The rate of change of the normalized Resonant Raman intensityis compared against the rate of change of normalized laser intensity. Inorder to minimize measurement errors, this comparison can be made atmultiple normalized rates of changes of laser intensity. To eliminateany systematic differences between the control parameter used tomodulate laser intensity and the resultant laser modulation, the laserpower was characterized by using a reference composition that provides acharacteristic Raman spectrum whose intensity does not change with laserpower. In one example, NIST SRM 2242 was used which provides a broadRaman spectrum with 532 nm light. An example of non-linear ResonantRaman spectroscopy according to the present disclosure is depicted inFIG. 1.

The slope of the trace in FIG. 1 is the calculated net signal. If theslope is not equal to 1, then it indicates that the 2^(nd) term in

${\frac{1}{I_{R}}\frac{\delta\; I_{R}}{\delta\; t}} = {{\frac{1}{I_{o}}\frac{\delta\; I_{o}}{\delta\; t}} + \frac{\delta\;\ln\mspace{14mu}\Sigma{\left( \alpha_{ij} \right)_{mn}}^{2}}{\delta\; t}}$

Equation 2 (the polarizability terms) is not equal to zero. This caneither indicate a change being brought about by the laser itself, or achange being brought about by a physical or chemical change in thesample.

Example 1

FIG. 2 depicts an example of non-linear Resonant Raman spectroscopy forcharacterizing small changes in a composition. The samples containlycopene that is non-covalently associated into albumin (as described inU.S. Patent Publication No. 2016/0324933, the disclosure of which isherein incorporated by reference), to which a nutritional buffer wasadded to support microbial metabolism, and a buffer that maintains thepH at 7.2.

In these examples, non-linear Resonant Raman spectroscopy measures theResonant Raman spectrum of lycopene and the magnitude of the Raman peaksare a sensitive function of small changes in the composition. Since thelycopene is incorporated into albumin, the non-linearity of the ResonantRaman response (i.e., the calculated non-linear Resonant Ramancoefficient) characterizes the environment provided by albumin, andsince albumin is designed to solubilize molecules that are insoluble inwater, the non-linearity of the Resonant Raman will respond to theamount of insoluble molecules present in the solution.

In this example, the amount of gases present in the sample ischaracterized by the non-linearity of the Resonant Raman response.Common gases (like oxygen, nitrogen and carbon dioxide) are somewhatsoluble in water, with the solubility decreasing as temperatureincreases. Thus, when one, or more parts of the test sample are heatedto a high temperature (such as 55° C.) for long enough, then thedissolved gases become supersaturated and nucleate out via a timedependent process. When this liquid is then cooled to 37° C., the liquidbecomes undersaturated with respect to the dissolved gases. If thisundersaturated liquid is mixed in with the album in/lycopene reagentthat is nominally stored at 4° C. (and is therefore saturated with gasesat 4° C., and supersaturated at 37° C.), then the mixture can becomeundersaturated with respect to the dissolved gases. In this scenario,some of the dissolved gases that had partitioned into albumin willmigrate to the solution, and reduce the amount of gases incorporatedinto albumin. Thus, by varying the amount of the undersaturated liquid(and the degree of undersaturation), the environment around the lycopeneis varied, and is characterized by changes in the Resonant Ramannon-linearity.

FIG. 2 illustrates the non-linearity of the Resonant Raman non linearitycoefficient with respect to different liquid formulations that allcontain the album in/lycopene reagent. The first example depicts acomparison between the reagent that has been stored at 5° C. for severalweeks, and tested at 37° C. (and is therefore supersaturated with gasesat 37° C.). The non-linearity coefficient of the reagent itself is 3.3.When bacteria (at a concentration of 10 CFU/mL) is added to thesolution, the non-linearity coefficient increases to 3.7

Example 2

Bilirubin is a powerful antioxidant present in serum and has very weakoptical absorption at 532 nm. In this example, bilirubin is used tocontrol the signal in non-linear Resonant Raman spectroscopy and is usedto improve signal-to-noise ratio when characterizing test samples.

In the samples described, bilirubin is added and is non-covalentlyassociated with an albumin protein. FIGS. 3 and 4 depict the effect ofbilirubin on the average Resonant Raman peak intensity. FIG. 3 depictsthe average Raman peak height from 4 uninfected control samples and 3samples infected with 10 CFUs of S. aureus. In all cases, the reagentincludes lycopene incorporated into albumin and diluted into 4 mL ofbuffer medium and containing 0.5× of a nutritional broth to enablebacteria metabolism. FIG. 4 depicts the average Raman peak height from 4uninfected control samples and 3 samples infected with 10 CFUs of S.aureus with 1 μM of added bilirubin. By comparison with FIG. 3, the dipin the infected samples has moved out to longer timescales (450 vs 200seconds), and the uninfected control sample does not show a dip anylonger.

FIG. 5 depicts determining the signal-to-noise ratio for the abovedescribed samples. In this example, the “signal” is the difference inthe average rates of change of the intensity of Resonant Raman peaks,computed using a linear fit from t=0 to the time denoted on the X axis,for the uninfected control samples and those with 10 CFU of S. aureus;and “noise” is the sum of the standard deviations around the averagerates of change for the control and 10 CFU samples. The signal-to-noiseratio is plotted as a function of time (on the X axis) and the amount ofadded bilirubin (in μM, denoted in the legend). As more bilirubin isadded, the signal builds up more slowly, and is also less likely torevert to a negative value.

FIG. 6 depicts the signal from the above described samples, estimated attime=600 seconds, plotted as a function of added bilirubin (in μM,denoted in the legend). For this timescale, 1 μM bilirubin is determinedto be an optimized amount of bilirubin. At higher bilirubin levels, thesignal does not have sufficient time to build up, and at lower bilirubinlevels, the signal has already built up to it's maximum value and isdecaying down to lower levels.

Example 3

Without being bound to any particular theory or mechanism of action,bilirubin in the subject methods enhances the signal in non-linearResonant Raman spectroscopy by: (a) scavenging free radicals generatedby the laser light. This reduces the artifact that can interfere withthe signal, and so reduces the standard deviation around the controlsamples. Thus, the standard deviation around the average rates of changeof the lycopene peaks in uninfected samples decreases as bilirubin isadded to the assay (b) scavenging free radicals generated by themetabolic activity of the microorganism present in the sample. This canslow down the changes caused by the microorganism, in particular whenchanges to the sample are too rapid to observe cleanly in the absence ofbilirubin.

FIG. 7 shows a plot of the signal-to-noise ratio of samples that containlycopene non-covalently associated with an albumin protein and differentamounts of bilirubin as a function of data collection time. Thesignal-to-noise ratio is maximized along various points along the linedepicted in the figure, and attains a maximum value at different pointsalong the line. Variation of the signal to noise ratio SNR (where“Signal” is the difference between the average rate of change of thelycopene peaks for an uninfected control sample, and that in a sampleinfected with 10 CFUs of S aureus & “Noise” is the sum of the standarddeviations around the two averages) with the time of experiment. In allcases, the slopes are calculated from t=0 to the time indicated on the Xaxis, so an increase in the SNR reflects a decrease in the standarddeviations (which is due to a decrease in the confidence interval aroundthe estimated slopes). The signal to noise ratio is plotted against time(on the X axis) and for a varying amount of bilirubin present in theassay (in the legend, in μM). The signal to noise ratio decreases whenthe signal starts to decrease because the time dependent Raman profilein the infected samples show a dip ˜ for experiments conducted beyondthe timescale of this tip, the magnitude of the signal decreases.

FIG. 8 plots the time points at which signal to noise ratio is maximizedagainst the added bilirubin concentration. As the bilirubinconcentration is increased, the optimal timepoint increases, which makesthe diagnostic test more reliable. Bilirubin has an absorption spectrumthat is just slightly blue shifted for absorption at 532 nm. This meansthat while it does not contribute to the Raman signal in a significantmanner, it could have a 2^(nd) order effect via the Raman enhancement ordeenhancement effect. The intensity of a resonance Raman peak isproportional to the square of the scattering cross section. Thescattering cross section, in turn, is related to the square of thetransition dipole moment and thus usually follows the absorptionspectrum. However, if there is another electronic state nearby, theRaman intensity is proportional to the square of the sum of the crosssections. If the cross sections are of opposite sign, destructiveinterference can occur, resulting in resonance deenhancement. If bothbilirubin and lycopene are present in the albumin, then it is possiblethat destructive/constructive interference is occurring between theexcited states, and this interference is altered as bilirubin degradesby scavenging free radicals. It has been found that other free radicalscavengers (including hydrophilic ones such as glutathione and ascorbicacid and hydrophobic ones such as butylated hydroxytoulene incorporatedinto albumin) do not have a similar effect on the diagnostic signal.

Example 4

Uncontrolled variations in the laser power (or a drift in the laserpower) can bias the observed rates of change. To correct for this, areference standard (one whose normalized spectrum is not expected tochange with laser power) was incorporated into the instrument andmonitored concurrently with the samples being tested. This method can beused to characterize the actual drift in the laser power, which can bemultiplied with the previously calibrated nonlinearity coefficient tosubtract out the biasing error in the observed slopes. An example ofthis correction is illustrated in FIGS. 9a and 9b . FIGS. 9a and 9bdepicts the Variation in the measured values for 4 uninfected and 3infected samples, as a function of bilirubin content. FIG. 9a depictsthe values as they are measured, and FIG. 9b depicts the values afterthey have been corrected for the observed drift in laser power.

An example system includes 8 sample chambers, one chamber is to bereserved for a calibration standard, such as NIST Raman CalibrationStandard SRM 2242. The instrument monitors the spectrum from thiscalibration standard using the same optical components (spectrometers,fibers etc) and algorithms as that used to monitor the Raman spectrumfrom the test samples. From the measured spectra of the standard sample,we compute the rate of change of Raman intensity as a function of time.This is then multiplied by the RRNL coefficient that has been previouslyestimated for the reagent liquid. This is the offset factor. From therate of change of the Raman peaks, the offset factor is subtracted.

Additional control steps are also implemented to ensure that the laserpower performance is closer to the desired specifications. For the 532nm laser, the laser power output can drift due to small changes in heatdissipation and buildup. These changes can affect performance. Theselimitations can be mitigated with control schemes that limit the driftin laser performance, and that can also flag when the laser is driftingoutside of a specified range.

FIG. 10 depicts the normalized rate of change of the Raman spectrum fromthe NIST standard as a function of the normalized rate of change of theCCD shutter time (which affects laser power via thermal buildup withinthe external laser cavity). This control can be used to vary the laserpower, but it can also be used to check if the instrument is behavingwith respect to thermal buildup issues. If the observed rate of changeof the Raman spectrum from the NIST standard is outside of the 90%confidence band depicted in FIG. 10, then it implies that the thermalmanagement issues have not been sufficiently mitigated.

Example 5

An example system is illustrated in FIG. 11. The layout shown in FIG. 11depicts 8 chambers, each maintained at 35° C.-37° C. Chamber 1 includesa reference composition, such as NIST Standard SRM 2242. The systemcollects the spectrum for each chamber, and then rotates a circularstage to the next chamber. It collects one cycle of Raman spectra forall 8 chambers in 15-25 seconds, and then repeats the process for thenext cycle until it has acquired data over about 600 seconds.Alternatively, if sampling rates faster than 15 seconds are desired,then the system can collect data on one chamber for the full time periodrequired, and then move onto the next chamber.

FIG. 12 describes various subsystems that are designed to minimizethermal fluctuations in the laser cavity. These include (a) the use offans for blowing in external air, circulating it within the instrumentand then exhausting it (b) the use of a combination of resistive andPeltier heating elements that maintains the sample chamber at 35-37° C.without unduly affecting changes in the instrument chamber outside ofthe sample chamber (the Peltier elements move heat from the instrumentchamber to the sample chamber while the resistive elements adds heat toboth sample and instrument chambers) and (c) use of an appropriatelylong delay (about 1 hour) after the laser has been turned on beforeoperations.

In order to further minimize the thermal effects, additional controlsare implemented to check for instrument stabilization. FIG. 13 depictsone setup algorithm that checks for instrument stabilization. The NISTStandard SRM 2242 was used to calibrate the CCD in the spectrometer over1 hour. Briefly, this calibration involves collecting the spectrum forthe NIST Standard SRM 2242, and dividing the measured output against theoutput expected for this standard. This calibration was performed over 1hour. The ratio between the measured CCD output and the expected outputis the YCAL. Subsequent to this, all output from the CCD is divided byYCAL to provide an output that should be independent of instrumentalvariations. The YCAL was checked by repeating the measurement on thesame NIST SRM 2242 sample over 10 minutes. If the ratio between themeasured spectra for the NIST SRM 2242 (after calibrating with YCAL) andthe expected spectrum demonstrates any ripples, then it implies that theinstrument has drifted in the 1 hour and 10 minute timescale. This isillustrated in FIG. 14. In some instances, the instrument stabilizesitself about 1-2 hours after the laser has been turned on.

In order to further minimize thermal management issues during instrumentoperation, one example includes utilization of control methods andalgorithms as depicted in FIG. 15. Light is admitted to the samplechamber via a mechanical shutter that is normally closed. When thisshutter is opened, the thermal management within the optical trainchanges. A short duration of time (e.g., ˜300 msec) elapses for thechanges to stabilize. Eight discrete spectra are acquired over 120 mseceach (for a total data collection time of about 1 sec), instead ofacquiring 1 spectrum over 1 sec. Variations within these 8 spectra arechecked and if the individual time periods have been properly adjusted,then the 8 spectra will demonstrate small systematic changes betweenthem.

Example 6

Experimental details for non-linear Resonant Raman spectroscopyaccording to certain embodiments of the subject methods are providedbelow.

Sample Preparation

Samples for non-linear Resonant Raman spectroscopy were prepared asdescribed in U.S. Patent Publication No. 2016/0324933. Briefly, lycopenethat is non-covalently associated with albumin in the samples wasextracted from tomatoes. Tomato paste is mixed with hexane, and theportion of the paste that dissolves in hexane is decanted off, and driedto powder. The composition is then refluxed over ethyl acetate, anddissolved in acetone. The acetone solution is mixed with an aqueoussolution of albumin, and the acetone is gradually removed with arotovapor. The process is monitored to ensure that all acetone isremoved, thereby ensuring that the organic extract from tomato istransferred to albumin. Additional specifications include (1) ensurethat there is no supersaturated gases in the reagent by incubating thebuffer solution at a temperature of about 60° C. for over 24 hours (atemperature over 50° C. for over 24 hours is also suitable). Since thegas solubility decreases at elevated temperatures, prolonged incubationat elevated temperatures ensures that the dissolved gases will crash outof the system via a process of nucleated bubble formation. The buffer iscooled to 37° C., and is used to finalize the reagent. At 37° C., thebuffer is undersaturated with respect to dissolved gases. This procedureensures that there are no excess gases in the final reagent. (2) Activeglutathione GSH is added to the reagent (as a reducing agent) andincubated for 18 hours or more and up to 5 days prior to use. Tests ofthe samples exhibit an increase in signal magnitude over time forincubation as well as added active glutathione. FIG. 16 depicts that themagnitude of the signal (defined as normalized rate of decrease of theRaman trace) from samples that contain 10 CFUs of added S. aureus in a4.5 mL test sample. The signal increases with increasing glutathionelevel. For these tests, the testing was performed within 2 hours of GSHaddition. FIG. 17 depicts the signal (difference in the rate of changeof the average control sample and samples with 10 CFU/mL plasma/Saureus) at 1700 seconds measurement time. The “incubation time” on the Xaxis refers to the time when the GSH was added (concentration in thelegend) to the reagent vial, and prior to the addition of infectedplasma for testing.

Preparation of a Zwitterionic-Coated Glass Vial

A glass vial is coated with a special zwitterion layer. To 30.03 gm(0.246 mol) of 1,3-propanesultone was added 200 mL of acetone with amagnetic stirrer bar under nitrogen gas. After vigorous stirring for 3min, and 50.0 gm (0.241 mmol) of3-(N,N-dimethylaminopropyl)trimethoxysilane through a syringe. Theresulting mixture was stirred vigorously overnight under N₂ gas. Afteradding another 100 mL of acetone, the mixtures were shaken well, andorganic solvents were removed by rotavapor and the white product wasfurther dried over a high vacuum pump very quickly (the desired productis highly hydroscopic). The white powder product was quickly transferredinto another plastic bottle and weighed to give 78.5 gm (98.9%) of thezwitterions silane reagent.

250 clear glass vials (Pacific Vial Catalogue #VC151965, dia=18.75 mm, 3DRAM) and the corresponding caps were rinsed once with deionized water,and autoclaved for 30 min. After cooling to room temperature, the glassvials are dried in an 80° C. oven and the autoclaved glass vials aretransferred to a 6 quart aluminum pressure cooker. To this is added 5 Lof autoclaved deionized water, 5 g of the zwitterions silane reagent (asdescribed above). The pressure cooker is capped and shaken by hand toensure that each vial is soaked with the silane solution. The cap isopened, and a visual inspection is made to ensure that each vial iscovered with the solution. The pressure cooker is capped and shaken for45 min. Next, another 5 g of the zwitterions silane reagent is added,and the handshaking/inspection/45 min shaking step is repeated. Theprocedure is repeated another 2 times, so that the total amount of thezwitterions silane reagent was 20 gm. The pressure cooker is then placedin an 80° C. oven for 2 hours (and up to 4 hours). The pressure cookeris then cooled to room temperature, opened and the aqueous solutiondecanted off. The glass vials are washed twice with autoclaved deionizedwater and once with ethanol/autoclaved deionized water (3:1 v/v) anddried in an 80° C. oven. After cooling to room temperature, the glassvials were transferred into a plastic bag and sealed for storage.

Laser Power

Without being bound to any particular theory or mechanism of action, thelaser power and exposure time can affect Resonant Raman spectroscopyaccording to the subject methods via one of several mechanisms:

At very large laser exposure times, the height of the Raman peaks incontrol samples can start to decrease while the sum of pixels remainslargely invariant. The laser's energy shifts the contributions thatcomprise the overall Raman peaks, and this shift results in a decreasein the observed peak height.

At very low laser exposure times, the read noise on the CCD canoverwhelm small effects are which one is attempting to monitor. Sincethe Raman effect is non-linear, large changes in laser power (e.g.,fluctuations in laser power) can result in changes in the observed Ramanamplitude being dominated by changes in the laser power (and thus makingit impossible to discern the effect of any bacteria presence).

In some embodiments, suitable laser exposure conditions for practicingthe subject methods include one that results in a maximum CCD count ofabout 10,000 to 40,000. In one example, the maximum saturation for theCCD is 65536 counts (corresponding to 16 bits), so this mode ofoperation results in a CCD that is well below saturation, but that alsooperates well above the region where read noise is an issue. In certaininstances, the mode of operation results in a total laser exposure ofabout 1 second (broken up into 4 CCD exposures of 0.25 seconds each;with each 0.25 second exposure resulting in a max CCD count of about30,000). At longer laser exposures, the observed peak heights decreaseover time, and at shorter laser exposures, they increase over time. Oneway to mitigate this effect is by working with the area under the curve(which remains relatively invariant, as depicted in FIG. 18), butworking with a 1 second laser exposure helps reduce this problemfurther. In particular, FIG. 18 depicts the rate of change of the Ramanpeak height and the “area under the curve” of the Raman peak heightcomputed as the sum of all the pixels (SOP in the legend) that describethe Raman peak. As the laser exposure time increases above 1 second foreach cycle of exposure, the Raman peak heights decrease significantly.By contrast, the area under the curve remains relatively invariant.

Detection and Signal Measurement System

The measurement system includes a spectrometer (equipped with acryogenically cooled CCD detector, capable of low dark currentoperation) and a laser light source (532 nm incident wavelength and 100mW power) that is capable of performing resonant Raman spectroscopy, asample chamber that includes a rotary table that can switch between upto 8 samples, a NIST SRM 2242 standard that is used to calibrate theinstrument, and a computer with appropriate software for controls andanalysis.

One illustrative method includes the following steps: (1) irradiatingthe sample with the monochromatic light source (e.g., at 532 nm), (2)measuring the scattered light intensity profile between 535 and 600 nm(and converting wavelength to wavenumbers), (3) calibrating the CCDoutput with a calibration constant developed from the NIST standard SRM2242, (4) separating the Raman contribution from the fluorescentbackground using an appropriate software algorithm, (5) repeating steps1-4, and characterizing the rate of change of the Raman peaks as afunction of time until the desired signal to noise ratio is attained (6)performing any necessary corrections for any systemic biases in the rateof change and (7) using the corrected rate of change to diagnose thesample based on preset threshold values.

Detection and Signal Measurement System: Alignment of the CollimatingLens

In some embodiments, the subject systems include a collimating lens thatfocuses light from the monochromatic light source onto the sample andcollects light scatter from the sample vial. If this lens is placed tooclose to the glass vial, then some of the scattered light can be lostoutside of the collection area of the lens. Further, the magnitude ofthis loss can change with small changes in the laser beam position (orwith mode hopping). Thus, when the lens position is sub-ideal, largechanges in the measured Raman intensity may be present due to thiseffect. By systematically varying the collimating lens position, asuitable position is determined to be where the focal spot is about 0.4mm deep into liquid layer within the glass vial, as shown in FIG. 19.FIG. 19 depicts the variation of the confidence interval of the NISTprofile as a function of distance between the edge of the glass-liquidlayer and the focal spot of the collimating lens.

To characterize the collimating lens position, the position of the lensis varied and scattered light is measured. Starting from the glasswalls, as the focal spot is moved into the liquid layer, the Ramanintensity increases at first (as the focal spot covers more of theliquid), and then decreases (as the scattered light is attenuated by theabsorption within the liquid). FIG. 20 depicts the variation of theRaman intensity profile as a function of collimating lens position forsample chambers 2-8 (sample chamber 1 is reserved for the NISTstandard). The intensity is maximized at position 5.65 mm, whichcorresponds to the edge of the glass-liquid interface. The nature of theinterface depends on the surface layer on the glass vial. FIG. 21illustrates the use of the Zwitterionic layer (as described above) tomake the measurement more robust against small changes in the focal spotposition. FIG. 21 depicts the slope of the uninfected control samples,as a function of the focal spot position from the edge of the glassliquid layer. For uncoated samples, the slope changes significantly withposition of the focal spot. For the glass vials that are coated with theZwitterion layer, the slope appears to be independent of focal spotposition, indicating that the interfacial layer extends deeper into theliquid.

(1) For uncoated glass vials, a significant signal is present at shorttimes. But this signal rapidly decreases to zero, and can even reverseitself for longer times, as illustrated in FIGS. 22A and 22B. (2) ForZwitterion coated samples, the signal to noise ratio continues to buildup over time. Thus, for the uncoated glass vials, reasonable signals canbe attained, but can depend on the position of the focal spot and thetime of signal recordation. For coated glass vials, the measurement isfound to be significantly more robust. FIG. 22A depicts thesignal-to-noise ratio of Zwitterion-coated and FIG. 22B depicts thesignal-to-noise ratio of uncoated glass vials, both measured with thefocal spot 0.4 mm from the glass surface. For the Zwitterion-coatedvials, the SNR builds up steadily over time. For the uncoated vials,there is a significant signal at about 900 seconds, but this signalrapidly decreases to zero and even reverses itself for longer times.

Detection and Signal Measurement System: Flow at the Sample-ContainerInterface

If the volume of sample irradiated by the monochromatic light source ischanged for every spectra acquired for that sample vial, then therewould be no laser induced non-linear Raman Resonant signals that can bemeasured. To ensure that the same volume of sample is measured thefollowing steps are taken: (a) maintaining the glass vial and the sampletherein at or nearly at complete rest so that the optical system probesthe same volume at every measurement; (b) ensuring that the opticalsystem is probing a volume that is close to the glass surface. There isan interfacial layer at the glass-liquid interface, where the relativevelocity of the liquid layer is close to zero. If this volume is probed,then this sampled volume will remain nearly invariant over multiplemeasurements. However, the results become very sensitive to both thenature of the interface layer, and the exact positioning of thecollimating lens. If the focal spot of the collimating lens is not deepenough, then error is possible due to laser mode hopping. If the focalspot is too deep, then the sampled volume may change due to motion, andthis will reduce the signal magnitude (or perhaps even flip italtogether). Based on these considerations, a suitable location of thecollimating lens in certain embodiments is about 0.2 mm from the edge ofthe glass-liquid layer. FIG. 23 depicts the variation of the signal tonoise ratio, estimated as the difference between the measured rate ofchange of the Raman peaks in 4 control samples and 3 with plasma thathas 10 CFU/mL of S aureus, and then divided by the rms standarddeviation. As the collimating lens is moved deeper into the liquidlayer, the Signal becomes smaller and effectively disappears. Further,the signal is also short lived ˜ it can be measured at 900 seconds, butis very small at 2500 seconds. This behavior is typical of uncoatedglass vials. The nature of the interfacial layer can be manipulated byapplying a coating on the glass surface. As discussed above, theapplication of a Zwitterionic layer on the glass surface extends theinterfacial layer deeper into the bulk sample volume.

Example Instrument Sequence of Operation

The control software instructs the spectrometer to “open” the mechanicalshutter (i.e., to expose the test sample to laser light). After a delayof 0.05 seconds (to allow the shutter motion), the CCD is instructed toinitiate data collection for 1.6 seconds. The CCD data is then shiftedinto the read electronics, and acquired by the laptop computer.

The instrument instructs the sample stage to rotate, such that the NISTcalibration standard (in Chamber 1) is exposed to the light path for 1.6seconds. It then instructs the rotary stage to move to the next chamber,and exposes the sample in that chamber. This process is repeated untilthe instrument has acquired one spectrum for all 7 chambers (if loaded)and the NIST calibration standard. This set of 8 measurements is calleda cycle, and typically takes 26 seconds.

The instrument performs testing over 33 minutes (over 75 testing cycles,with each cycle taking 26 seconds). The first 5 cycles are “darkcycles”, wherein the mechanical shutter is not opened. These 5 darkcycles give the instrument (laser/CCD etc) an opportunity to stabilize.After these 5 cycles, the mechanical shutter opens when instructed to doso during a cycle.

For each spectrum acquired, the software initiates a set of mathematicalalgorithms to analyze the data. (1) First, it subtracts the “darkcurrent” from the CCD output, and converts the X axis on the resultantspectra from pixel number to frequency using a predefined linearconversion factor. (2) Next, it multiplies the raw CCD output with thecalibration factor, thereby providing a spectrum that is nominallyindependent of instrument to instrument variations. (3) Third, itimplements an algorithm based on the Lieber method to estimate thebackground fluorescence. (4) It then detects the peak in the spectralprofiles at 1156, 1516 and 4000 cm-1 (the major peaks associated withthe example biomarker; the last one is ignored for plasma samples), (5)Finally, the height and area under the curve for these peaks are storedin a table, and used in subsequent analysis steps.

The software starts computing the slope of the line defined by thesedata points. This is done by fitting the data (peak height and areaunder the curve versus time, separately and independently for both the1516 and 1156 cm-1 peaks and also for the 4000 cm-1 peak) using a linearleast square fitting algorithm that comes standard with NationalInstrument LabView packages. This algorithm also computes the 95%confidence interval (95% CI) around the slope and y intercept values.From this slope, the slope of the fluorescent background at 3000 cm⁻¹ issubtracted ˜ this normalization step removes any systemic biases to thedata introduced by distortions to the interfacial layer caused by largeparticle clumps.

The algorithm compares the slopes (along with the 95% CI around theslope) to a decision threshold that has been set via previous testing.The threshold is set to slope >−0.5×10⁻⁵/sec for diagnosing uninfectedsamples (samples with observed slopes greater than this value arediagnosed as being uninfected) and slope <−1.5×10⁻⁵/sec for diagnosinginfected samples (samples with observed slopes less than this value arediagnosed as being infected) at a time period of 600 seconds ˜ observedthat for infected samples, the signal decays inversely with time.Samples that have a slope between these two values are diagnosed as“dichotomous”. For diagnostic purposes, the average slope is computedfrom the 1156, 1516 and 4000 (if available) cm⁻¹ Raman peaks.

Example Software Algorithm for Separating Raman and Fluorescence SignalContributions

Algorithms for maximizing test performance are implemented. The Liebermethod is used to subtract background fluorescence. This method isillustrated in FIG. 24 which depicts the Lieber method for fitting a 5thorder polynomial to a spectra that comprises contributions from Ramanpeaks and background fluorescence. The raw measured spectrum is fittedto a 5th order polynomial. The data points in the Input spectrum thatare higher than the fitted polynomial are replaced by the fittedpolynomial, and the modified spectrum is fitted to a new polynomial. Incertain embodiments of the subject methods, the Lieber method isoptimized by: (a) the Lieber method is implemented on the firstspectrum. For background fluorescence, a 5^(th) order polynomial (insome instances, a 4^(th) order polynomial is used) between thewavenumbers 1050 and 1650 cm⁻¹; (b) for subsequent spectra, thebackground fluorescence fit (i.e., the 5^(th) order polynomial, above)is used with its amplitude varied. The approach of constraining the fitensures that the results do not include amplified mathematicalartifacts.

Laser Power Fluctuations and Instrument Errors

In embodiments, the rate of change of the Raman peaks as a function oftime is measured. These measurements can be affected by changes in thelaser power, and in various instabilities in the alignment of theinstrument. Uniform drifts in the laser power can be corrected via theNIST standard, but higher order instabilities cannot be corrected withthe NIST standard. Characterization of the instabilities (which include,potentially, laser mode hopping, and drifts in the position of any ofthe alignment lenses during the test) is however helpful to flagmeasurements that are suspect.

To do this, the output from the NIST standard is characterized and theslope and confidence interval of that slope are measured at the end ofan experiment. When working with artificially spiked samples, the Signalto Noise Ratio was found to vary with both the slope, and CI of theslope, as shown in FIG. 25. Specifically, FIG. 25 depicts variation ofthe Signal to noise ratio at the end of the measurement, with thecollimating lens at the ideal position, and with coated glass vialsbeing used in all measurements. Each SNR value represents onemeasurement set with 4 uninfected control samples, and 3 with plasmainfected to 10 CFU/mL of added S. aureus. The measurements are repeated,and the SNR is plotted as a function of the confidence interval of theestimated slope of the NIST standard (top) and the slope itself(bottom).

Thus, measurements when the NIST profile is “clean” (i.e., where the SNRis expected to be >1), the CI of the NIST slope is less than 0.25, andthe slope itself is between −1 and 0.1×10-5/sec are then considered forfurther analysis.

Example 7: Characterizing the Presence of a Microorganism in a Sample

Determining the presence or absence of a pathogenic microorganism isdepicted in FIG. 26. The example depicts the use of a test withartificially spiked samples that are created as follows: (a) first, astock solution of S. aureus in buffer is prepared with a concentrationof 1000 CFU/mL. 0.05 mL of this stock solution (or, an expected 50 CFUs)is added to 5 mL of plasma purchased from a blood bank and incubated for2 hours. (b) 0.6 mL of this infected plasma is added to the standardreagent formulation that has a volume of 3.9 mL. Three “infected”samples are created from this plasma. (c) Four uninfected controlsamples are created by adding 0.6 mL of uninfected plasma (that has alsobeen subject to 2 hour incubation) to the reagent formulation. All 7test vials are tested simultaneously, with the results illustrated inFIGS. 26A-26C. Use of these known samples enables the use of simplestatistical measures (such as signal to noise) to characterize themeasurement.

While the test is running, the heights of the Raman peaks arecontinuously monitored, and their rate of change, for individual testvials. FIGS. 26A-26C illustrates these measurements as aggregates forcontrol and infected samples. For the infected sample, Raman peaksdecrease slowly over time. FIG. 26A depicts the amplitude of the Ramanpeaks, aggregated for the 4 uninfected control samples and the 3infected samples. The rate of change of the area under the curve isshown in FIG. 26B. The signal is defined as the difference between therate of change of the uninfected control, and the infected sample. Theuninfected control samples demonstrate a rate of change that isconsistent with the rate of change observed on the NIST standard ˜ whichis estimated to be (0.59±0.16)×10⁻⁵/sec at the end of the measurement.FIG. 26C depicts the signal-to-noise ratio, estimated as the signaldivided by the rms standard deviation of the rate of change ofuninfected and infected samples.

For final diagnosis, this value is subtracted from the estimated slopes,which reduces the aggregate control slope (and also values forindividual vials) slightly below the zero line, as illustrated in FIG.27. Specifically, FIG. 27 depicts the estimated slopes aggregated forcontrol and infected values and corrected for the variation observed inthe NIST standard. After correcting for the drift in the NIST profiles,and collecting data for a long enough time period such that the SNR>>1,the samples can be analyzed to determine if a pathogenic microorganismis present. Bacterial cells are added to the plasma and the infectedplasma is added to the standard reagent. Similar results are observedwhen bacterial cells are added to the plasma, incubated for 2 hours, andcentrifuged at high speed (12 krpm, 5 mins) so as to remove thebacterial cells (this removal is verified by culture on broth media)from the plasma, and this infected/centrifuged plasma is added to thereagent vial.

Example 8: Infected Samples without Pathogens

In clinical scenarios, the effect of sampling volume needs to beconsidered. Most patients with a bloodstream infection have a bloodpathogen concentration of about 1-10 CFU/mL. Further, the volume ofblood sampled during the blood draw is generally limited to about 10 mLor so (and often less). Thus, for several infected patients, it isexpected that 0 CFUs will be present in the blood draw simply due toPoisson sampling statistics. The methods described herein would still beable to identify those samples as “infected” because the subject methodscan detect free radicals generated by the bacteria, and not just thebacteria itself.

To demonstrate this, a 2nd experiment is discussed below where theprotocol is as follows: (a) first, a stock solution of S. aureus inbuffer is prepared with a concentration of 1000 CFU/mL. 0.05 mL of thisstock solution (or, an expected 50 CFUs) is added to 5 mL of plasmapurchased from a blood bank and incubated for 2 hours. (b) This plasmais centrifuged at 12000 rpm for 5 minutes so as to remove the bacteriafrom the plasma. The plate count method is used to characterize thepathogen concentration in the plasma before and after thecentrifugation. (c) 0.6 mL of this infected plasma is added to thestandard reagent formulation that has a volume of 3.9 mL. 3 “infected”samples are created from this plasma. (d) 4 uninfected control samplesare created by adding 0.6 mL of uninfected plasma (that has also beensubjected to 2 hour incubation) to the reagent formulation. All 7 testvials are tested simultaneously, with the results illustrated in FIG.28A-28C. FIG. 28A depicts the estimated rate of change for theuninfected and infected samples, estimated from the area under thecurve. The signal is defined as the difference between the rate ofchange of the uninfected control, and the infected sample. FIG. 28Bdepicts signal-to-noise ratio, estimated as the signal divided by therms standard deviation of the rate of change of uninfected and infectedsamples. FIG. 28C depicts signal, as a function of time for this sampleset in which the bacteria has been centrifuged and removed. Also shownfor comparison is a sample set that does not have the centrifugationstep to remove the bacteria. As is clear from the traces, the signal isweaker when the bacteria has been centrifuged out, and also decreasesinversely with time. By contrast, when the bacteria is present in thetest sample, then the signal decays with the square root of time.

Example 9: Characterizing Clinical Samples

For clinical samples (i.e., those that include plasma from humanpatients), a number of additional factors are further considered, e.g.,the plasma can contain clumps of various proteins and lipids that candistort the flow at the interface and/or cause other changes thatapplies a systematic bias to the data. To normalize these biases, theslope of the fluorescence output is considered (e.g., at 3000 cm⁻¹). Analgorithm used for normalization is as follows:

-   -   (a) First, compute the slope of the Raman peaks using the        methods described above.    -   (b) Next, compute the slope of the fluorescent output at 3000        cm⁻¹. If this slope is less than a certain predefined threshold,        then reject the measurement as being too noisy. In this case,        this threshold is set to be −4.5×10⁻⁵/sec.    -   (c) If the slope of the fluorescent output is less than the        threshold, then subtract this value from the slope of the Raman        peaks. This is the “signal”.    -   (d) Account for samples that may have a very low amplitude to        begin with ˜ this can be for any number of reasons, including        the presence of a large number of red blood cells in the plasma,        the aggregation of a large number of albumin molecules etc. The        algorithm flags these samples as infected, so as to prevent the        possibility of false negatives that can harm the patient.    -   (e) Samples are diagnosed as infected if either the final slope        (after subtracting the fluorescence slope) is less than        −1×10⁻⁵/sec, or the amplitude of the Raman peaks is less than        0.22 (where the NIST profile=1). Samples are diagnosed as        uninfected if both the final slope (measured at 1000 seconds) is        greater than −0.8×10⁻⁵/sec and the amplitude of the Raman peak        is greater than 0.22. The slope threshold is significantly        greater than the threshold suggested by the scaling behavior        without bacteria present (ca. −0.25×10⁻⁵/sec) but slightly less        than the scaling behavior with bacteria present (−1×10⁻⁵/sec).

One illustrative example is depicted in FIGS. 29A and 29B. The resultsfrom the subject rapid test methods are compared with the results fromblood culture. The tests are done on discarded plasma samples obtainedfrom the remnants of the CBC (complete blood count) test done onpatients who are suspected of having a bloodstream infection (and forwhom a blood culture test was also ordered). After the CBC test is done,the CBC test vacutainer is retrieved and 0.6 mL from the plasma layer isaliquoted (some of these plasma samples had a significant amount of redcoloration due to remnant red blood cells). The 0.6 mL of the plasmalayer is added to the reagent that had glutathione (GSH) of 0.3 mL andwhich had been incubated at 37° C. for 18 hours. The test vials wereplaced in the test instrument and tested immediately. FIG. 29A depictsthe rate of change of the Raman peaks and FIG. 29B depicts the amplitudeof the Raman peaks for a set of tests done with added plasma fromdifferent patients. With the above-described algorithm, the samples arediagnosed as infected if either the Amplitude (FIG. 29B), or the Slope(FIG. 29A) are in the “infected” band. The overall detection metrics areas follows:

-   -   (a) 40 samples that were diagnosed as “negative” by the subject        methods described herein, and that were also blood culture        negative. “40 true negatives”    -   (b) 0 samples that were diagnosed as blood culture positive that        were diagnosed as negative by the subject methods described        herein. “0 False negatives”    -   (c) 6 samples that were blood culture positive and that were        also diagnosed as positive by the subject methods described        herein. “6 true positives”    -   (d) 7 samples that were blood culture negative and that were        diagnosed as positive by the subject methods described herein.        “7 false positives”    -   (e) 13 samples that were blood culture negative, but for which        the subject methods described herein were unable to make any        diagnosis (either because the slopes were in the intermediate        range, or because the fluorescence slope was changing outside of        the set threshold). 4 samples were blood culture positive, but        for which no diagnosis was determined by the subject methods.

With these settings, for infected samples, the rate of change of theRaman peaks correlates with the time to positivity in the blood culturetest, as depicted in FIG. 30.

A comparison of the signal magnitude over time for different sampletypes is presented in FIGS. 31A and 31B. Specifically, FIG. 31A depictsthe signal magnitude (rate of change of Raman peaks in uninfectedcontrol samples minus the rate of change of Raman peaks in infectedsamples) for multiple test runs summarizing the variation of the signalwith time for different sample types. In all cases, the signal magnitudedecays inversely with time. Multiple runs are demonstrated with 10CFU/mL S. aureus present in the test sample. FIG. 31B depicts the signalstrength at 1000 seconds for different sample types. When the bacteriaare centrifuged out, then the signal appears to be smaller. The signalappears be significantly higher in the clinical samples.

Further, the signal strength in the clinical samples appears to besignificantly greater than that in samples with 10 CFU/mL of S. aureuspresent in the test sample, even with 2 hours of incubation. Since theclinical samples are expected to have 1-10 CFU/mL pathogenconcentration, and since only 0.6 mL of plasma is sampled, it isbelieved that many of the clinical samples do not have any activebacteria present in them. Given the large signal magnitude in theseclinical samples, it is clear that the methods described herein areresponding to the free radicals generated by bacteria.

Example 10: Measuring the Minimal Inhibitory Concentration ofAntimicrobial Agents

To measure the minimum inhibitory concentration, or to otherwisecharacterize the antimicrobial susceptibility of any unknown pathogen toa candidate antimicrobial:

-   -   (a) Incubate the unknown pathogen for about 3 hours in a rich        media. This time period should suffice to increase the        concentration of the causative pathogen by about >100×. Thus,        the 1 CFU (or more) in the original sample will become >100        CFUs.    -   (b) Aliquot the pathogen into about 7 equal parts, and each part        will be expected to have at least 14 CFUs, which is sufficiently        greater than the poisson sampling error of square root of the        number of expected CFUs (14, in this case).    -   (c) To each part, add a variable concentration of the candidate        antimicrobial, starting at very low concentrations of 0.125        μg/mL, and increasing in steps of 2 to 0.25, 0.5, 1, 2, 4 & 8        μg/mL (this range is designed to span the desired MIC in 7 steps        of 2). Incubate this mixture for another 20 minutes, which        allows for sufficient time for the 10 CFUs to interact with the        candidate antimicrobial.    -   (d) Add the 7 mixtures to the test vials, and test. The number        of free radicals present in the mixed sample is a function of        the concentration of the antimicrobial, and so the final slope        can be plotted against antimicrobial concentration to develop        estimates for the MIC. This is illustrated in FIGS. 32A and 32B.

FIG. 32A depicts the measured slope as a function of antimicrobial agent(vancomycin) concentration. FIG. 32B depicts the time taken for thetested samples to become cloudy. Above 2 μg/mL, the samples remain clearfor very long incubation periods (>96 hours). Thus, the MinimumBactericidal Concentration MBC is about 2 μg/mL. Above 0.25 mg/mL, thetime to cloudiness increases slightly. Thus, the MIC is about 0.25mg/mL. As illustrated in FIGS. 32A and 32B, the MIC corresponds to theconcentration at which the signal decreases slightly. Further, the MBC(Minimum Bactericidal Concentration) corresponds to the concentration atwhich the signal increases again.

Example 11: Methods for Determining the Phenotype of an UnknownMicroorganism

The phenotype of an unknown microorganism in a sample can be determinedby employing an added crosslinking agent. Below, a peptidase isidentified in the sample by adding a crosslinking agent that includes acleavable peptide bond next to a glutamic acid group. The synthesis of aglutamic acid derivative with disulfide crosslinkers is shown in Scheme1.

Compound 1: Into a 250 mL round bottom flask containing a magneticstirring bar, were added 3.0 gm (26.4 mmole) of cysteamine hydrochloride(Sigma-Aldrich, cat. #: M6600) and 60 mL of methanol. The mixture wasstirred at a magnetic stirrer to form a solution. Into this solution wasadded 6.2 gm (28.2 mmole) of 2, 2′-dithioldipyridine (Sigma-Aldrich,cat. #: 43791) portion by portion. The resulting yellow solution wasstirred overnight and concentrated to dry powder using a Rotavapor. Theyellow product was further dried over a high vacuum pump for 4 to 5 h togive 9.03 gm of a yellow powder product (with about 98.2% yield). Thisproduct mixtures contained unreacted starting material, 2,2′-dithioldipyridine, the desired product, compound 1 and the sideproduct, 2-thiolpyridine. Without further purifications, the productmixture was used for the next step reaction. Compound 2: Into a 250 mLround bottom flask containing a magnetic stirring bar, were added 0.5 gm(2.0 mmole) of BOC-L-glutamic acid (Sigma-Aldrich, cat. #: 16345), 0.86gm (4.5 mmole) of EDAC [N-(3-dimethylaminopropyl)-N′-ethylcarbodiimdehydrochloride, Sigma-Aldrich, cat. #: E7760), 0.52 gm (4.5 mmole) of NHS(N-hydroxysuccinimide, Sigma-Aldrich, cat. #: 56480) and 40 mL ofdichloromethane. The mixture was stirred at a magnetic stirrer for 2 hand the clear solution was formed. Into this solution was added 4 mL ofTEA (trimethylamine, EMD, cat. #: 1200-5) and 100 mg of DMAP[4-(dimethylamino)pyridine, Aldrich, cat. #: 10,770-0), and then 1.4 gmof Compound 1 mixtures. The reaction mixtures were stirred overnight andwashed three times with 30 mL of 5% NaHCO₃ aqueous solution, the bottomsolution was dried over sodium sulfate. After the solvents were removedvia a Rotovapor and the product residue was dissolved on 5 mL of CH₂Cl₂for column purifications. 30 gm of silica gel was loaded with CH₂Cl₂ andthe crude product solution was loaded onto the column, and the columnwas eluted with CH₂Cl₂, 1% CH₃OH/CH₂Cl₂ and 2% CH₃OH/CH₂Cl₂, 3%CH₃OH/CH₂Cl₂. The fractions were identified by the normal phase TLCplates, developing with 5% CH₃OH/CH₂Cl₂ (Rf=0.28). The desired fractionswere pooled and concentrated to give 0.28 gm (0.48 mmole) of thesemisolid Compound 3, 22.2% in yield. ¹H NMR spectra in CDCl₃ matches tothe proposed structure of Compound 3.

Compound 4: Into a 100 mL round bottom flask containing a magneticstirring bar, was added 0.28 gm (0.48 mmole) of Compound 3, 15 mL ofmethanol and 3 mL of concentrated hydrochloric acid solution. Theresulting mixture was stirred for 15 min, and concentrated to smallvolume by a Rotavapor (mostly water). The product residue was furtherdried over a high vacuum to dryness. After adding about 3 mL of ethanol,the product mixture was further over a high vacuum to give 0.29 (0.479mmole) gm of the powder product, Compound 4, 99.8% in yield. Withoutfurther purifications, the product can be dissolved in water and the pHwas adjusted to 5.3 using 0.1 mM NaOH solution, which is used forcrosslinking the proteins, such as albumin, through the disulfideexchanges by the cysteine residue of proteins with the activateddisulfide.

The crosslinker increases the background UV-Vis absorption as depictedin FIG. 33A, however the UV-Vis absorption decreases over time for highcrosslinker content (the albumin network is being reshuffled by theGSH). FIG. 33A depicts the effect of absorbance at 650 nm for a peptidecrosslinker that contains two disulfide bonds that exchange with thereduced disulfide bonds on the albumin, thereby creating a network ofalbumin molecules. The background absorbance from albumin (from Rayleighscattering) increases with crosslinker content (correspondingly, ourreagent test vials that contain the crosslinker demonstrate a signalsimilar to what is observed with pathogenic microorganisms). Certainbacteria produce a peptidase that can cleave the glutamic acid peptidebond (e.g., S. aureus), resulting in an increase in the Raman signalover time (FIG. 33B). This rate of this increase scales with pathogenconcentration. This corresponds to the Raman test results as well, asdepicted in FIG. 34. At low crosslinker content, the Raman peaksdecrease over time, consistent with the formation of an albumin network.At high crosslinker content, the Raman peaks increase. In certainembodiments, the crosslinked albumin network is reduced back tomonomeric albumin by a bacterial metabolite (the peptidase in thecurrent case). For example, for testing a peptidase, crosslinker:albuminratio was set at 1:2.

Upon mixing with albumin, the disulfide bonds on the crosslinkerexchanges with the cysteine groups on the albumin, and creates albumindimers. In turn, this increases the background absorbance due toRayleigh scattering (FIG. 33A). For reagent systems with very largeamounts of crosslinkers, it appears that the crosslinked albuminreshuffles the disulfide bonds over time, and slowly reduces theRayleigh scattering. Thus, in these experiments, the crosslinker:albuminratio was set to 1:2. For this system, Raman peaks decrease in amplitudeover time, resembling the albumin crosslinking brought about by freeradicals. If a reagent system that contains the peptide disulfidecrosslinker is exposed to peptidase producing bacteria, then thecleavage of the crosslinker will result in a disruption of the interfacelayer, and an increase in the Raman peak amplitude. This suggests aninoculum dependence with a limit of detection better than 10 CFUs in 4mL reagent. (FIG. 33B).

Example 12: Detection and Characterization Via Fluorescence

Determining the presence or absence of a pathogenic microorganism isdepicted in FIGS. 35A and 35B. The example depicts the use of a testwith artificially spiked samples that are created as follows: (a) first,a stock solution of S. aureus in buffer is prepared with a concentrationof 1000 CFU/mL. 0.05 mL of this stock solution (or, an expected 50 CFUs)is added to 5 mL of plasma purchased from a blood bank and incubated for2 hours. (b) This plasma is then centrifuged to remove the bacteria fromthe plasma. 0.6 mL of this infected plasma is added to the standardreagent formulation that has a volume of 3.9 mL. Three “infected”samples are created from this plasma. (c) Three uninfected controlsamples are created by adding 0.6 mL of uninfected plasma (that has alsobeen subject to 2 hour incubation and then centrifuged) to the reagentformulation. (d) One reagent control sample vial is created by takingthe reagent vial without any additions. All 7 test vials are testedsimultaneously, with the results illustrated in FIGS. 35A-B. Use ofthese known samples enables the use of simple statistical measures (suchas signal to noise) to characterize the measurement.

While the test is running, the fluorescence values at a suitablefrequency is continuously monitored, and their rate of change, forindividual test vials is calculated. FIG. 35A illustrates thesemeasurements as aggregates for control and infected samples, and alsothat for the single reagent control sample. FIG. 35A depicts thefluorescence values, aggregated for the 3 uninfected control samples,the 3 infected samples and the reagent sample. The fluorescence valuesin the uninfected control samples decrease due to the process offluorescence quenching. The rate of decrease in the infected samples issomewhat greater than this. The signal is defined as the differencebetween the rate of change of the fluorescence in uninfected controlsample and that in the infected sample. The uninfected control samplesdemonstrate a rate of change that is consistent with the rate of changeobserved on reagent control sample ˜ which is estimated to be(−2.2±0.1)×10⁻⁵/sec at the end of the measurement in this example. FIG.35B depicts the signal-to-noise ratio, estimated as the signal dividedby the rms standard deviation of the rate of change of uninfected andinfected samples.

For final diagnosis, the rate of change of the fluorescence in thereagent vial is subtracted from the rate of change of fluorescence inthe test vials. After correcting for the drift in the reagent controlstandard, and collecting data for a long enough time period such thatthe SNR>>1, the samples can be analyzed to determine if a pathogenicmicroorganism is present.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it is readily apparent to those of ordinary skill in theart in light of the teachings of this disclosure that certain changesand modifications may be made thereto without departing from the spiritor scope of the appended claims.

Accordingly, the preceding merely illustrates the principles of theinvention. It will be appreciated that those skilled in the art will beable to devise various arrangements which, although not explicitlydescribed or shown herein, embody the principles of the invention andare included within its spirit and scope. Furthermore, all examples andconditional language recited herein are principally intended to aid thereader in understanding the principles of the invention being withoutlimitation to such specifically recited examples and conditions.Moreover, all statements herein reciting principles, aspects, andembodiments of the invention as well as specific examples thereof, areintended to encompass both structural and functional equivalentsthereof. Additionally, it is intended that such equivalents include bothcurrently known equivalents and equivalents developed in the future,i.e., any elements developed that perform the same function, regardlessof structure. The scope of the present invention, therefore, is notintended to be limited to the exemplary embodiments shown and describedherein. Rather, the scope and spirit of present invention is embodied bythe appended claims.

1-22. (canceled)
 23. A system comprising: (a) a monochromatic lightsource; (b) an optical adjustment component; (c) a photodetector; and(d) a processor comprising memory operably coupled to the processorwherein the memory comprises instructions stored thereon, which whenexecuted by the processor, cause the processor to: irradiate a sample ina sample holder with the monochromatic light source with either aninvariant light intensity or one that varies over time at an interfacebetween the sample and a surface of the sample holder; measure scatteredlight from the sample with the photodetector at a plurality of differenttimes; determine the intensity of Resonant Raman scattering andfluorescence scattering; calculate a rate of change in the intensity ofResonant Raman scattering and the intensity of fluorescence scattering;and correct the calculated rate of change of the intensity of ResonantRaman scattering and the intensity of fluorescence scattering to obtaina net signal.
 24. The system according to claim 23, wherein the opticaladjustment component comprises collimating optics mounted on a lineartable that is configured to produce an adjustable focal spot.
 25. Thesystem according to claim 23, wherein the optical adjustment componentfurther comprises a mechanical shutter.
 26. The system according toclaim 23, further comprising a rotary table with a plurality of samplechambers.
 27. The system according to claim 26, wherein the rotary tablecomprises 8 sample chambers.
 28. The system according to claim 27,further comprising a subsystem for characterizing incoherently scatteredlight, wherein the subsystem comprises: collimating optics; and opticaladjustment components configured to spread the incoherently scatteredlight onto a linear array of photodetectors.
 29. The system according toclaim 28, wherein the processor further comprises memory withinstructions stored thereon, which when executed by the processor, causethe processor to move the collimating optics to focus light on each ofthe sample chambers.
 30. The system according to claim 23, wherein thesample further comprises an albumin with an incorporated ligand.
 31. Thesystem according to claim 23, wherein the memory further comprisesinstructions which when executed by the processor, cause the processorto: determine a rate of change in the intensity of fluorescentscattering (or any other optical output) from the reagent vial;calculate a net signal as the rate of change in the intensity of theResonant Raman scattering minus the rate of change in the intensity offluorescent scattering from the standard sample.
 32. The systemaccording to claim 23, wherein the memory further comprises instructionswhich when executed by the processor, cause the processor to: determinea rate of change in total output from a standard reference sample;calculate a net signal as the rate of change in the intensity of theResonant Raman scattering minus the rate of change in the intensity ofResonant Raman scattering from the standard sample.
 33. The systemaccording to claim 31, wherein the memory further comprises instructionswhich when executed by the processor, cause the processor to compare thenet signal with preset thresholds, and to determine that the sampleincludes actively metabolizing microorganisms based on the comparison.34. The system according to claim 23, wherein the sample furthercomprises a reducing agent.
 35. The system according to claim 34,wherein the sample further comprises a disulfide crosslinking agent. 36.The system according to claim 35, where the disulfide crosslinking agentfurther comprises a core that is cleaved by enzymes or a metaboliteproduced by the microorganism in the sample.
 37. The system according toclaim 35, wherein the crosslinking agent comprises a compound of Formula(I):


38. The system according to claim 23, wherein the sample holder is aglass vial.
 39. The system according to claim 23, wherein the sampleholder further comprises a coating that modifies albumin absorption. 40.The system according to claim 39, wherein the coating comprises aZwitterionic coating.
 41. The system according to claim 23, wherein theprocessor is configured to expose the sample to the monochromatic lightsource to minimize the net signal.
 42. (canceled)
 43. The systemaccording to claim 42, wherein the system is configured to maximize thenet signal.